Изучим, как реализован контроль температуры в молекулярной динамике на примере GROMACS. Объект исследования - одна молекула этана.
Предоставлен gro файл(http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro) с координатами этана.
Подготовим файл топологии et.top. Есть заготовка, куда нужно вписать номера атомов, образующих связи, плоские и торсионные углы.
In [1]:
# загрузим модули
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem, Draw
from rdkit.Chem import Descriptors
from rdkit import RDConfig
from IPython.display import Image,display
import numpy as np
In [2]:
# создадим этан
mol=Chem.MolFromSmiles('CC')
AllChem.Compute2DCoords(mol)
m3d=Chem.AddHs(mol)
Chem.AllChem.EmbedMolecule(m3d)
AllChem.MMFFOptimizeMolecule(m3d,maxIters=500,nonBondedThresh=200)
Out[2]:
0
In [6]:
# и придумаем циклы
## связи
bonds = m3d.GetBonds()
for i,b in enumerate(bonds):
print b.GetBeginAtomIdx()+1 , b.GetEndAtomIdx()+1
1 2 1 3 1 4 1 5 2 6 2 7 2 8
In [10]:
## углы
for b1 in m3d.GetBonds():
for b2 in m3d.GetBonds():
if b1.GetBeginAtomIdx() == b2.GetBeginAtomIdx() and b1.GetIdx() != b2.GetIdx():
print ' ',b1.GetEndAtomIdx()+1,' ',b1.GetBeginAtomIdx()+1,' ',b2.GetEndAtomIdx()+1,' ','1'
2 1 3 1
2 1 4 1
2 1 5 1
3 1 2 1
3 1 4 1
3 1 5 1
4 1 2 1
4 1 3 1
4 1 5 1
5 1 2 1
5 1 3 1
5 1 4 1
6 2 7 1
6 2 8 1
7 2 6 1
7 2 8 1
8 2 6 1
8 2 7 1
In [21]:
## торсионные углы: с повторами, в файле убрала одинаковые углы
for b1 in m3d.GetBonds():
for b2 in m3d.GetBonds():
for b3 in m3d.GetBonds():
if b1.GetBeginAtomIdx() == b2.GetBeginAtomIdx() and b1.GetIdx() != b2.GetIdx() and b2.GetEndAtomIdx()==b3.GetBeginAtomIdx() and b3.GetIdx() != b2.GetIdx():
print ' ',b1.GetEndAtomIdx()+1,' ',b1.GetBeginAtomIdx()+1,' ',b2.GetEndAtomIdx()+1,' ',b3.GetEndAtomIdx()+1,' ','3'
3 1 2 6 3 3 1 2 7 3 3 1 2 8 3 4 1 2 6 3 4 1 2 7 3 4 1 2 8 3 5 1 2 6 3 5 1 2 7 3 5 1 2 8 3
Посмотрим, какой тип атома у углерода в этане: есть строчка такая:
opls_067 15.03500 ; CH3 (C1) ETHANE
такая:
opls_139 12.01100 ; alkane C
и такая:
opls_140 1.00800 ; alkane H.
Возьмем два соседних номера, 139 и 140.
In [22]:
%%bash
cat /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
; OPLS atom types and masses. ; Atom types are named opls_X, where X is the OPLS number. ; The opls_ prefix is to avoid users confusing atom types ; (always prefixed) with atom numbers in molecules (never prefixed). ; ; Types 1-134 are from the united-atom OPLS, which can be ; useful for solvents and/or CH2 optimizations (e.g. in lipids). ; Explicit all-atom parameters start with opls_135. ; Note: For UA amide parameters - ; NMA - types 1,2,3,4,7,39 ; Formamide 131,2,12,13 ; DMF 131,2,3,132 ; Acetamide 1,2,7,12,13 ; ; Types 1-65 are united-atom parameters for proteins, ; see JACS 110, 1657 (1988). ; opls_001 12.01100 ; opls_002 15.99940 ; opls_003 14.00670 ; opls_004 1.00800 ; opls_005 14.02700 ; opls_006 13.01900 ; opls_007 15.03500 ; opls_008 13.01900 ; opls_009 14.02700 ; opls_010 15.03500 ; opls_011 12.01100 ; opls_012 14.00670 ; opls_013 1.00800 ; opls_014 13.01900 ; opls_015 14.02700 ; opls_016 14.02700 ; opls_017 12.01100 ; opls_018 15.99940 ; opls_019 14.02700 ; opls_020 14.00670 ; opls_021 1.00800 ; opls_022 14.02700 ; opls_023 15.99940 ; opls_024 1.00800 ; opls_025 13.01900 ; opls_026 12.01100 ; opls_027 14.02700 ; opls_028 14.02700 ; opls_029 13.01900 ; opls_030 13.01900 ; opls_031 14.02700 ; opls_032 32.06000 ; opls_033 1.00800 ; opls_034 14.02700 ; opls_035 32.06000 ; opls_036 15.03500 ; opls_037 14.02700 ; opls_038 32.06000 ; opls_039 15.03500 ; opls_040 14.00670 ; opls_041 1.00800 ; opls_042 14.00670 ; opls_043 12.01100 ; opls_044 12.01100 ; opls_045 12.01100 ; opls_046 14.00670 ; opls_047 1.00800 ; opls_048 12.01100 ; opls_049 12.01100 ; opls_050 12.01100 ; opls_051 14.00670 ; opls_052 1.00800 ; opls_053 12.01100 ; opls_054 14.00670 ; opls_055 1.00800 ; opls_056 14.02700 ; opls_057 14.02700 ; opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester opls_060 13.01900 ; opls_061 14.02700 ; opls_062 15.99940 ; O- in COOR ester opls_063 15.03500 ; CH3 in COOCH3 opls_064 12.01100 ; opls_065 15.03500 ; opls_066 16.04300 ; CH4 JACS,106,6638 (1984) opls_067 15.03500 ; CH3 (C1) ETHANE opls_068 15.03500 ; CH3 (C2) N-ALKANES opls_069 15.03500 ; CH3 (C3) ISOBUTANE opls_070 15.03500 ; CH3 (C4) NEOPENTANE opls_071 14.02700 ; CH2 (SP3) ALKANES opls_072 14.02700 ; CH2 (SP2) 1-ALKENES opls_073 13.01900 ; CH (SP3) ISOBUTANE opls_074 13.01900 ; CH (SP2) 2-ALKENES opls_075 13.01900 ; CH (AROM) BENZENOID united atom opls_076 12.01100 ; C (SP3) NEOPENTANE opls_077 12.01100 ; C (SP2) ISOBUTENE opls_078 15.99940 ; O ALCOHOLS JPC,90,1276 (1986) opls_079 1.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) opls_081 14.02700 ; CH2 IN ETHANOL JPC,90,1276 (1986) opls_082 32.06000 ; S IN H2S JPC,90,6379 (1986) opls_083 32.06000 ; S IN RSH JPC,90,6379 (1986) opls_084 32.06000 ; S IN RSR JPC,90,6379 (1986) opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) opls_086 1.00800 ; H IN H2S JPC,90,6379 (1986) opls_087 1.00800 ; H(S) IN RSH JPC,90,6379 (1986) opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986) opls_092 15.03500 ; CH3 IN CH3SSR JPC,90,6379 (1986) opls_093 14.02700 ; CH2 IN RCH2SSR JPC,90,6379 (1986) opls_094 14.00670 ; N IN CH3CN Mol.Phys.,63,547 (1988) opls_095 12.01100 ; C IN CH3CN Mol.Phys.,63,547 (1988) opls_096 15.03500 ; CH3 IN CH3CN Mol.Phys.,63,547 (1988) opls_097 39.94800 ; Argon from Verlet & Weis Mol.Phys.,24,1013 (1972) For Ne and He, opls_098 83.79800 ; Krypton from Verlet & Weis Mol.Phys.,24,1013 (1972) see types 129,130. opls_099 131.29300 ; Xenon from Verlet & Weis Mol.Phys.,24,1013 (1972) opls_101 14.00670 ; N (NH4+) JPC,90,2174 (1986) opls_102 14.00670 ; N (RNH3+) JPC,90,2174 (1986) opls_103 14.00670 ; N (R4N+) JPC,90,2174 (1986) opls_104 1.00800 ; H (NH4+) JPC,90,2174 (1986) opls_105 1.00800 ; H (RNH3+) JPC,90,2174 (1986) opls_106 15.03500 ; United-atom CH3 (CH3NH3+) JPC 90,2174 (1986) opls_107 15.03500 ; United-atom CH3 ((CH3)4N+) JPC 90,2174 (1986) opls_108 15.99940 ; United-atom Ether O JCC,11,958 (1990) opls_109 15.03500 ; United-atom Ether CH3 (-O) JCC,11,958 (1990) opls_110 14.02700 ; United-atom Ether CH2 (-O) JCC,11,958 (1990) opls_111 15.99940 ; O TIP3P Water opls_112 1.00800 ; H TIP3P Water opls_113 15.99940 ; O TIP4P Water opls_114 1.00800 ; H TIP4P Water opls_115 0.00000 ; M TIP4P Water opls_116 15.99940 ; O SPC Water opls_117 1.00800 ; H SPC Water opls_118 15.99940 ; O TIP5P Water opls_119 1.00800 ; H TIP5P Water opls_120 0.00000 ; L TIP5P Water opls_122 12.01100 ; C CCl4 opls_123 35.45300 ; Cl CCl4 opls_124 32.06000 ; S in UA DMSO opls_125 15.99940 ; O in UA DMSO opls_126 15.03500 ; CH3 in UA DMSO opls_127 14.00670 ; Updated ammonia parameters - JPC B 2001, 105, 6474 opls_128 1.00800 ; Updated ammonia parameters - JPC B 2001, 105, 6474 opls_129 20.17970 ; Neon Hirschfelder (Wiley,1954) opls_130 4.00260 ; Helium Hirschfelder (Wiley,1954) opls_131 12.01100 ; C in C=O for UA formamide, DMF. opls_132 15.03500 ; CH3 in HCON(CH3)2 DMF opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_137 12.01100 ; alkane CH opls_138 12.01100 ; alkane CH4 opls_139 12.01100 ; alkane C opls_140 1.00800 ; alkane H. opls_141 12.01100 ; alkene C (R2-C=) opls_142 12.01100 ; alkene C (RH-C=) opls_143 12.01100 ; alkene C (H2-C=) opls_144 1.00800 ; alkene H (H-C=) opls_145 12.01100 ; Benzene C - 12 site JACS,112,4768-90. Use #145B for biphenyl opls_145B 12.01100 ; Biphenyl C1 opls_146 1.00800 ; Benzene H - 12 site. opls_147 12.01100 ; Naphthalene fusion C (C9) opls_148 12.01100 ; C: CH3, toluene opls_149 12.01100 ; C: CH2, ethyl benzene opls_150 12.01100 ; diene =CH-CH=; use #178 for =CR-CR= opls_151 35.45300 ; Cl in alkyl chlorides opls_152 12.01100 ; RCH2Cl in alkyl chlorides opls_153 1.00800 ; H in RCH2Cl in alkyl chlorides opls_154 15.99940 ; all-atom O: mono alcohols opls_155 1.00800 ; all-atom H(O): mono alcohols, OP(=O)2 opls_156 1.00800 ; all-atom H(C): methanol opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols opls_158 12.01100 ; all-atom C: CH, alcohols opls_159 12.01100 ; all-atom C: C, alcohols opls_160 12.01100 ; CH2 Trifluoroethanol opls_161 12.01100 ; CF3 Trifluoroethanol opls_162 15.99940 ; OH Trifluoroethanol opls_163 1.00800 ; HO Trifluoroethanol opls_164 18.99840 ; F Trifluoroethanol opls_165 1.00800 ; H Trifluoroethanol opls_166 12.01100 ; C(OH) phenol Use with all opls_167 15.99940 ; O phenol atom C, H 145 & 146 opls_168 1.00800 ; H phenol opls_169 15.99940 ; O: diols opls_170 1.00800 ; H(O): diols opls_171 15.99940 ; O: triols opls_172 1.00800 ; H(O): triols opls_173 12.01100 ; C(H2OH): triols opls_174 12.01100 ; C(HROH): triols opls_175 12.01100 ; C(R2OH): triols opls_176 1.00800 ; H(CXOH): triols opls_178 12.01100 ; diene =CR-CR=; use #150 for =CH-CH= opls_179 15.99940 ; O: anisole opls_180 15.99940 ; O: dialkyl ether opls_181 12.01100 ; C(H3OR): methyl ether opls_182 12.01100 ; C(H2OR): ethyl ether opls_183 12.01100 ; C(HOR): i-Pr ether, allose opls_184 12.01100 ; C(OR): t-Bu ether opls_185 1.00800 ; H(COR): alpha H ether opls_186 15.99940 ; O: acetal ether opls_187 15.99940 ; O(H): hemiacetal opls_188 1.00800 ; H(O): hemiacetal opls_189 12.01100 ; C(H2O2): acetal OCH2O opls_190 1.00800 ; H(CHO2): acetal OCH2O opls_191 12.01100 ; C(H2O2): hemiacetal OCH2OH opls_192 1.00800 ; H(CHO2): hemiacetal OCH2OH opls_193 12.01100 ; C(HCO2): acetal OCHRO opls_194 1.00800 ; H(CHO2): acetal OCHRO opls_195 12.01100 ; C(HCO2): hemiacetal OCHROH opls_196 1.00800 ; H(C2O2): hemiacetal OCHROH opls_197 12.01100 ; C(C2O2): acetal OCRRO opls_198 12.01100 ; C(C2O2): hemiacetal OCRROH opls_199 12.01100 ; C(O,Me): anisole opls_200 32.06000 ; all-atom S: thiols opls_201 32.06000 ; S IN H2S JPC,90,6379 (1986) opls_202 32.06000 ; all-atom S: sulfides, S=C opls_203 32.06000 ; all-atom S: disulfides opls_204 1.00800 ; all-atom H(S): thiols opls_205 1.00800 ; H IN H2S JPC,90,6379 (1986) opls_206 12.01100 ; all-atom C: CH2, thiols opls_207 12.01100 ; all-atom C: CH, thiols opls_208 12.01100 ; all-atom C: C, thiols opls_209 12.01100 ; all-atom C: CH3, sulfides opls_210 12.01100 ; all-atom C: CH2, sulfides opls_211 12.01100 ; all-atom C: CH, sulfides opls_212 12.01100 ; all-atom C: C, sulfides opls_213 12.01100 ; all-atom C: CH3, disulfides opls_214 12.01100 ; all-atom C: CH2, disulfides opls_215 12.01100 ; all-atom C: CH, disulfides opls_216 12.01100 ; all-atom C: C, disulfides opls_217 12.01100 ; all-atom C: CH3, methanethiol opls_218 12.01100 ; C in CH2OH - benzyl alcohols opls_219 12.01100 ; C in CHROH - benzyl alcohols opls_220 12.01100 ; C in CR2OH - benzyl alcohols opls_221 12.01100 ; C(CH2OH) - benzyl alcohols opls_222 32.06000 ; S in thioanisoles opls_223 12.01100 ; C in RCH2NH2. Use #223B for AA Calpha. opls_223B 12.01100 ; Gly Calpha opls_224 12.01100 ; C in R2CHNH2. Use #224B for AA Calpha. opls_224B 12.01100 ; Calpha in most AA (except Gly,Pro,Aib) opls_225 12.01100 ; C in R3CNH2. Use #225B for AA Calpha. opls_225B 12.01100 ; Aib Calpha. opls_226 35.45300 ; chloroalkene Cl (ClH-C=) - see also #398 opls_227 12.01100 ; chloroalkene C (ClH-C=) opls_228 12.01100 ; C(SMe) thioanisole opls_229 12.01100 ; C on N: secondary N-CHR2 amide opls_230 12.01100 ; C on N: secondary N-CR3 amide opls_231 12.01100 ; C: C=O in benzophenone opls_232 12.01100 ; C: C=O in benzaldehyde,acetophenone (CH) opls_233 12.01100 ; C: C=O in acetophenone (CMe) opls_234 12.01100 ; C: C=O in benzamide opls_235 12.01100 ; C=O in amide, dmf, peptide bond opls_236 15.99940 ; O: C=O in amide. Acyl R on C in amide is neutral - opls_237 14.00670 ; N: primary amide. use alkane parameters. opls_238 14.00670 ; N: secondary amide, peptide bond (see #279 for formyl H) opls_239 14.00670 ; N: tertiary amide opls_240 1.00800 ; H on N: primary amide opls_241 1.00800 ; H on N: secondary amide opls_242 12.01100 ; C on N: secondary N-Me amide opls_243 12.01100 ; C on N: tertiary N-Me amide opls_244 12.01100 ; C on N: secondary N-CH2R amide opls_245 12.01100 ; C on N: tertiary N-CH2R amide, Pro CD opls_246 12.01100 ; C on N: tertiary N-CHR2 amide, Pro CA opls_247 12.01100 ; C in O=C(NH2)2 Urea opls_248 15.99940 ; O in O=C(NH2)2 Urea Isr. J. Chem opls_249 14.00670 ; N in O=C(NH2)2 Urea 33, 323 (93) opls_250 1.00800 ; H in O=C(NH2)2 Urea opls_251 14.00670 ; N in imide opls_252 12.01100 ; C(=O) in imide opls_253 15.99940 ; O in imide opls_254 1.00800 ; H(N) in imide opls_255 1.00800 ; H(C) in formimide opls_256 12.01100 ; C in CH3 imide opls_257 12.01100 ; C in RCH2 imide opls_258 12.01100 ; C in R2CH imide opls_259 12.01100 ; C in R3C imide opls_260 12.01100 ; C(CN) benzonitrile opls_261 12.01100 ; C(N) benzonitrile opls_262 14.00670 ; N benzonitrile opls_263 12.01100 ; C(Cl) chlorobenzene opls_264 35.45300 ; Cl chlorobenzene opls_265 14.00670 ; N: N-phenylacetamide opls_266 12.01100 ; ipso C in N-phenylacetamide opls_267 12.01100 ; Co in CCOOH carboxylic acid opls_268 15.99940 ; Oh in CCOOH R in RCOOH is opls_269 15.99940 ; Oc in CCOOH neutral; use #135-#140 opls_270 1.00800 ; H in CCOOH opls_271 12.01100 ; C in COO- carboxylate opls_272 15.99940 ; O: O in COO- carboxylate,peptide terminus opls_273 12.01100 ; C: CH3, carboxylate ion opls_274 12.01100 ; C: CH2, carboxylate ion opls_275 12.01100 ; C: CH, carboxylate ion opls_276 12.01100 ; C: C, carboxylate ion opls_277 12.01100 ; AA C: aldehyde - for C-alpha use #135-#139 opls_278 15.99940 ; AA O: aldehyde opls_279 1.00800 ; AA H-alpha in aldehyde & formamide opls_280 12.01100 ; AA C: ketone - for C-alpha use #135-#139 opls_281 15.99940 ; AA O: ketone opls_282 1.00800 ; AA H on C-alpha in ketone & aldehyde opls_283 12.01100 ; CA on C-terminal ALA,CYS,SER,THR,HIS,ASP,ASN opls_284 12.01100 ; CA on C-terminal GLY opls_285 12.01100 ; CA on C-terminal PRO opls_286 14.00670 ; N (NH4+) JPC,90,2174 (1986) opls_287 14.00670 ; N (RNH3+) JPC,90,2174 (1986) opls_288 14.00670 ; N (R4N+) JPC,90,2174 (1986) opls_289 1.00800 ; H (NH4+) JPC,90,2174 (1986) opls_290 1.00800 ; H (RNH3+) JPC,90,2174 (1986) opls_291 12.01100 ; C in CH3NH3+ opls_292 12.01100 ; C in RCH2NH3+ opls_292B 12.01100 ; CA in GLY-NH3+ N-term. opls_293 12.01100 ; C in R2CHNH3+ opls_293B 12.01100 ; CA in NH3+ N-term, All AA except GLY & PRO opls_294 12.01100 ; C in R3CNH3+ opls_295 12.01100 ; AA C-alpha on N-term PRO opls_296 12.01100 ; AA:C-delta in N-term PRO NH2+ opls_297 12.01100 ; CT in CH3NH2+R opls_298 12.01100 ; AA C-alpha in Gly zwitterion opls_299 12.01100 ; AA C-alpha in Ala zwitterion opls_300 14.00670 ; N: guanidinium NH2 opls_301 1.00800 ; H: guanidinium NH2 opls_302 12.01100 ; C: guanidinium C+ opls_303 14.00670 ; N: guanidinium NHR opls_304 1.00800 ; H: guanidinium NHR opls_305 12.01100 ; C: CH3, methylguanidinium opls_306 12.01100 ; C: CH3, ethylguanidinium opls_307 12.01100 ; C: CH2(D), ARG, ethylguanidinium opls_308 12.01100 ; C: CH2(G), ARG opls_309 14.00670 ; N (R2NH2+), N-terminal PRO NH2+ opls_310 1.00800 ; H (R2NH2+) opls_311 14.00670 ; DAP N1 (Diaminopyridine) opls_312 12.01100 ; DAP C2 opls_313 14.00670 ; DAP N-amine opls_314 1.00800 ; DAP H-amine opls_315 12.01100 ; DAP C3 opls_316 1.00800 ; DAP H3 opls_317 12.01100 ; DAP C4 opls_318 1.00800 ; DAP H4 opls_319 14.00670 ; Uracil & Thymine N1 - use #319B for nucleoside opls_319B 14.00670 ; Uracil & Thymine N1 - only for nucleoside opls_320 12.01100 ; Uracil & Thymine C2 opls_321 14.00670 ; Uracil & Thymine N3 opls_322 12.01100 ; Uracil & Thymine C4 opls_323 12.01100 ; Uracil & Thymine C5 opls_324 12.01100 ; Uracil & Thymine C6 opls_325 1.00800 ; Uracil & Thymine H-N1 opls_326 15.99940 ; Uracil O-C2 opls_327 1.00800 ; Uracil H-N3 opls_328 15.99940 ; Uracil O-C4 opls_329 1.00800 ; Uracil H-C5 opls_330 1.00800 ; Uracil H-C6 opls_331 12.01100 ; Thymine C-C5 opls_332 1.00800 ; Thymine H-CC5 opls_333 14.00670 ; Cytosine N1 -use #333B for nucleoside opls_333B 14.00670 ; Cytosine N1 - for nucleoside opls_334 12.01100 ; Cytosine C2 opls_335 14.00670 ; Cytosine N3 opls_336 12.01100 ; Cytosine C4 Nucleotide base opls_337 12.01100 ; Cytosine C5 parameters: opls_338 12.01100 ; Cytosine C6 JACS,113,2810(1991) opls_339 1.00800 ; Cytosine H-N1 opls_340 15.99940 ; Cytosine O-C2 opls_341 14.00670 ; Cytosine N-C4 opls_342 1.00800 ; Cytosine H-NC4/N3 opls_343 1.00800 ; Cytosine H-NC4/C5 opls_344 1.00800 ; Cytosine H-C5 opls_345 1.00800 ; Cytosine H-C6 opls_346 14.00670 ; Adenine N1 opls_347 12.01100 ; Adenine C2 opls_348 14.00670 ; Adenine N3 opls_349 12.01100 ; Adenine C4 opls_350 12.01100 ; Adenine C5 opls_351 12.01100 ; Adenine C6 opls_352 14.00670 ; Adenine & Guanine N7 opls_353 12.01100 ; Adenine & Guanine C8 opls_354 14.00670 ; Adenine & Guanine N9 - use #354B for nucleoside opls_354B 14.00670 ; Adenine & Guanine N9 - nucleoside only opls_355 1.00800 ; Adenine & Guanine H-C2 opls_356 14.00670 ; Adenine & Guanine N-C6 opls_357 1.00800 ; Adenine & Guanine H-NC6/N1 opls_358 1.00800 ; Adenine & Guanine H-NC6/C5 opls_359 1.00800 ; Adenine & Guanine H-C8 Guanine opls_360 1.00800 ; Adenine & Guanine H-N9 Guanine opls_361 14.00670 ; Guanine N1 opls_362 12.01100 ; Guanine C2 opls_363 14.00670 ; Guanine N3 opls_364 12.01100 ; Guanine C4 opls_365 12.01100 ; Guanine C5 opls_366 12.01100 ; Guanine C6 opls_367 1.00800 ; Guanine H-N1 opls_368 14.00670 ; Guanine N-C2 opls_369 1.00800 ; Guanine H-NC2 opls_370 15.99940 ; Guanine O-C6 opls_371 12.01100 ; 9-Me Adenine or Guanine C-N9 opls_372 1.00800 ; 9-Me Adenine or Guanine H-CN9 opls_373 12.01100 ; 1-Me Uracil or Thymine C-N1 opls_374 1.00800 ; 1-Me Uracil or Thymine H-CN1 opls_375 12.01100 ; 1-Me Cytosine C-N1 opls_376 1.00800 ; 1-Me Cytosine H-CN1 opls_377 14.00670 ; CytH+ N1 Use #377B for nucleoside. opls_377B 14.00670 ; CytH+ N1 - nucleoside only opls_378 12.01100 ; CytH+ C2 opls_379 14.00670 ; CytH+ N3 Protonated cytosine. opls_380 12.01100 ; CytH+ C4 opls_381 12.01100 ; CytH+ C5 opls_382 12.01100 ; CytH+ C6 opls_383 1.00800 ; CytH+ H-N1 opls_384 15.99940 ; CytH+ O-C2 opls_385 1.00800 ; CytH+ H-N3 opls_386 14.00670 ; CytH+ N-C4 opls_387 1.00800 ; CytH+ H-NC4/N3 opls_388 1.00800 ; CytH+ H-NC4/C5 opls_389 1.00800 ; CytH+ H-C5 opls_390 1.00800 ; CytH+ H-C6 opls_391 12.01100 ; 1-Me CytH+ C-N1 opls_392 1.00800 ; 1-Me CytH+ H-CN1 opls_393 30.97376 ; P dimethylphosphate anion UA - see #440 for AA opls_394 15.99940 ; O(=) dimethylphosphate anion UA - see #440 for AA opls_395 15.99940 ; O(-) dimethylphosphate anion UA - see #440 for AA opls_396 12.01100 ; C in CH3 dimethylphosphate anion UA - see #440 for AA opls_400 18.99840 ; F- JACS 106, 903 (1984) opls_401 35.45300 ; Cl- JACS 106, 903 (1984) opls_402 79.90400 ; Br- JACS 107, 7793(1985) opls_403 126.90450 ; I- JACS 120, 5104(1998) opls_404 6.94100 ; Li+ JACS 106, 903 (1984) opls_405 22.98977 ; Na+ JACS 106, 903 (1984) opls_406 6.94100 ; Li+ opls_407 22.98977 ; Na+ Aqvists cation opls_408 39.09830 ; K+ parameters: opls_409 85.46780 ; Rb+ JPC,94, 8021 (90) opls_410 132.90540 ; Cs+ opls_411 24.30500 ; Mg++ opls_412 40.08000 ; Ca++ opls_413 87.62000 ; Sr++ opls_414 137.33000 ; Ba++ opls_415 12.01100 ; C in CH3S- thiolate opls_416 1.00800 ; H in CH3S- opls_417 32.06000 ; S in CH3S- opls_418 12.01100 ; C in CH3O- alkoxide opls_419 1.00800 ; H in CH3O- opls_420 15.99940 ; O in CH3O- opls_421 12.01100 ; C1 in CH2CN- RCN- opls_422 1.00800 ; H in CH2CN- opls_423 12.01100 ; C2 in CH2CN- JACS 111,4190 (89) opls_424 14.00670 ; N in CH2CN- opls_425 12.01100 ; C in CH3NH- opls_426 1.00800 ; HC in CH3NH- RNH- opls_427 14.00670 ; N in CH3NH- opls_428 1.00800 ; HN in CH3NH- opls_429 12.01100 ; C2 in CH3CH2- RCH2- opls_430 1.00800 ; H in CH3CH2- opls_431 12.01100 ; C1 in CH3CH2- opls_432 1.00800 ; H1 in CH3CH2- opls_433 0.00000 ; LP in CH3CH2- opls_434 15.99940 ; O in OH- Hyroxide O-H = 0.953 A opls_435 1.00800 ; H in OH- JACS 108, 2517 (86) opls_436 0.00000 ; U in UO2+ J Mol Struct 366, 55 (96) opls_437 15.99940 ; O in UO2+ r(U-O) = 1.80 A opls_440 30.97376 ; P in Me2PO4-, Me2PO4H opls_441 15.99940 ; O= in Me2PO4-, Me2PO4H opls_442 15.99940 ; OMe in Me2PO4-, Me2PO4H dimethylphosphate opls_443 12.01100 ; C in Me2PO4-, Me2PO4H dimetylphosphate opls_444 1.00800 ; H in Me2PO4-, Me2PO4H 6-31+G* CHELPG opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 opls_450 30.97376 ; P in MePO3Me-, MePO3HMe opls_451 15.99940 ; O= in MePO3Me-, MePO3HMe opls_452 15.99940 ; OMe in MePO3Me-, MePO3HMe methyl opls_453 12.01100 ; C(O) MePO3Me-, MePO3HMe methylphosphonate opls_454 1.00800 ; H(CO) MePO3Me-, MePO3HMe 6-31+G* CHELPG opls_455 12.01100 ; C(P) MePO3Me-, MePO3HMe opls_456 1.00800 ; H(CP) MePO3Me-, MePO3HMe opls_457 12.01100 ; Cipso benzyl methylphosphonate opls_458 12.01100 ; C(O) benzyl methylphosphonate opls_459 1.00800 ; H(CO) benzyl methylphosphonate opls_460 12.01100 ; Cipso methyl benzylphosphonate opls_461 12.01100 ; C(P) methyl benzylphosphonate opls_462 1.00800 ; H(CP) methyl benzylphosphonate opls_463 12.01100 ; Cipso C6H5OPO3(2-) use with #445-#447 opls_465 12.01100 ; AA C: esters - for R on C=O, use #280-#282 opls_466 15.99940 ; AA =O: esters opls_467 15.99940 ; AA -OR: ester opls_468 12.01100 ; methoxy C in esters - see also #490-#492 opls_469 1.00800 ; methoxy Hs in esters opls_470 12.01100 ; Co in benzoic acid opls_471 12.01100 ; Co in methyl benzoate, aryl ester opls_472 12.01100 ; Cipso phenyl ester opls_473 15.99940 ; AA -OR phenyl ester opls_474 32.06000 ; S in sulfonamide, S(=O)2(OR) opls_475 15.99940 ; O in sulfonamide, S(=O)2(OR) opls_476 12.01100 ; CH3 attached to S of sulfonamide opls_477 1.00800 ; H of Me attached to S of sulfonamide opls_478 14.00670 ; N: primary amide of sulfonamide opls_479 1.00800 ; H on N: primary sulfonamide opls_480 14.00670 ; N secondary amide of sulfonamide opls_481 1.00800 ; H on N: secondary sulfonamide opls_482 12.01100 ; alpha CH3-N of sulfonamide opls_483 1.00800 ; H of alpha CH3-N of sulfonamide opls_484 12.01100 ; alpha CH2-N of sulfonamide. Use q=0.45 for CRH-N, q=0.65 for O=N-C-CH-N. opls_485 1.00800 ; H of alpha CH2-N of sulfonamide opls_486 12.01100 ; beta CH3 of N-ethyl sulfonamide opls_487 1.00800 ; H of beta CH3 of N-ethyl sulfonamide opls_488 12.01100 ; benzene C attached to S of sulfonamide opls_490 12.01100 ; C(H2OS) ethyl ester opls_491 12.01100 ; C(HOS) i-pr ester opls_492 12.01100 ; C(OS) t-bu ester opls_493 32.06000 ; S in sulfone opls_494 15.99940 ; O in sulfone opls_496 32.06000 ; sulfoxide - all atom opls_497 15.99940 ; sulfoxide - all atom opls_498 12.01100 ; CH3 all-atom C: sulfoxide opls_499 12.01100 ; CH2 all-atom C: sulfoxide opls_500 12.01100 ; CG in Trp opls_501 12.01100 ; CD C in Trp opls_502 12.01100 ; CE C in Trp opls_503 14.00670 ; NE in Trp opls_504 1.00800 ; H on NE in Trp opls_505 12.01100 ; CB in His opls_506 12.01100 ; CE1 in HID, HIE opls_507 12.01100 ; CD2 in HID, CG in HIE opls_508 12.01100 ; CG in HID, CD2 in HIE opls_509 12.01100 ; CE1 in HIP opls_510 12.01100 ; CG, CD2 in HIP opls_511 14.00670 ; NE in HID, ND in HIE opls_512 14.00670 ; N in HIP opls_513 1.00800 ; H on N in HIP opls_514 12.01100 ; CD1 in TRP opls_515 12.01100 ; all-atom C: CH, isopropyl benzene opls_516 12.01100 ; all-atom C: C, t-butyl benzene opls_517 12.01100 ; vinyl ether HCOR opls_518 12.01100 ; vinyl ether RCOR opls_520 14.00670 ; N in pyridine 6-31G* opls_521 12.01100 ; C1 in pyridine CHELPG opls_522 12.01100 ; C2 in pyridine charges opls_523 12.01100 ; C3 in pyridine for opls_524 1.00800 ; H1 in pyridine 520-619 opls_525 1.00800 ; H2 in pyridine opls_526 1.00800 ; H3 in pyridine opls_527 14.00670 ; N in pyrazine opls_528 12.01100 ; C in pyrazine opls_529 1.00800 ; H in pyrazine opls_530 14.00670 ; N in pyrimidine opls_531 12.01100 ; C2 in pyrimidine opls_532 12.01100 ; C4 in pyrimidine opls_533 12.01100 ; C5 in pyrimidine opls_534 1.00800 ; H2 in pyrimidine opls_535 1.00800 ; H4 in pyrimidine opls_536 1.00800 ; H5 in pyrimidine opls_537 14.00670 ; N in pyridazine opls_538 12.01100 ; C3 in pyridazine opls_539 12.01100 ; C4 in pyridazine opls_540 1.00800 ; H3 in pyridazine opls_541 1.00800 ; H4 in pyridazine opls_542 14.00670 ; N in pyrrole opls_543 12.01100 ; C2 in pyrrole opls_544 12.01100 ; C3 in pyrrole opls_545 1.00800 ; H1 in pyrrole opls_546 1.00800 ; H2 in pyrrole opls_547 1.00800 ; H3 in pyrrole opls_548 14.00670 ; N1 in pyrazole opls_549 14.00670 ; N2 in pyrazole opls_550 12.01100 ; C3 in pyrazole opls_551 12.01100 ; C4 in pyrazole opls_552 12.01100 ; C5 in pyrazole opls_553 1.00800 ; H1 in pyrazole opls_554 1.00800 ; H3 in pyrazole opls_555 1.00800 ; H4 in pyrazole opls_556 1.00800 ; H5 in pyrazole opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ; N3 in imidazole opls_560 12.01100 ; C4 in imidazole opls_561 12.01100 ; C5 in imidazole opls_562 1.00800 ; H1 in imidazole opls_563 1.00800 ; H2 in imidazole opls_564 1.00800 ; H4 in imidazole opls_565 1.00800 ; H5 in imidazole opls_566 15.99940 ; O in furan opls_567 12.01100 ; C2 in furan opls_568 12.01100 ; C3 in furan opls_569 1.00800 ; H2 in furan opls_570 1.00800 ; H3 in furan opls_571 15.99940 ; O in oxazole opls_572 12.01100 ; C2 in oxazole opls_573 14.00670 ; N in oxazole opls_574 12.01100 ; C4 in oxazole opls_575 12.01100 ; C5 in oxazole opls_576 1.00800 ; H2 in oxazole opls_577 1.00800 ; H4 in oxazole opls_578 1.00800 ; H5 in oxazole opls_579 15.99940 ; O in isoxazole opls_580 14.00670 ; N in isoxazole opls_581 12.01100 ; C3 in isoxazole opls_582 12.01100 ; C4 in isoxazole opls_583 12.01100 ; C5 in isoxazole opls_584 1.00800 ; H3 in isoxazole opls_585 1.00800 ; H4 in isoxazole opls_586 1.00800 ; H5 in isoxazole opls_587 14.00670 ; N1 in indole opls_588 12.01100 ; C2 in indole opls_589 12.01100 ; C3 in indole opls_590 12.01100 ; C4 in indole opls_591 12.01100 ; C5 in indole opls_592 12.01100 ; C6 in indole opls_593 12.01100 ; C7 in indole opls_594 12.01100 ; C8 in indole opls_595 12.01100 ; C9 in indole opls_596 1.00800 ; H1 in indole opls_597 1.00800 ; H2 in indole opls_598 1.00800 ; H3 in indole opls_599 1.00800 ; H4 in indole opls_600 1.00800 ; H5 in indole opls_601 1.00800 ; H6 in indole opls_602 1.00800 ; H7 in indole opls_603 14.00670 ; N1 in quinoline opls_604 12.01100 ; C2 in quinoline opls_605 12.01100 ; C3 in quinoline opls_606 12.01100 ; C4 in quinoline opls_607 12.01100 ; C5 in quinoline opls_608 12.01100 ; C6 in quinoline opls_609 12.01100 ; C7 in quinoline opls_610 12.01100 ; C8 in quinoline opls_611 12.01100 ; C9 in quinoline opls_612 12.01100 ; C10 in quinoline opls_613 1.00800 ; H2 in quinoline opls_614 1.00800 ; H3 in quinoline opls_615 1.00800 ; H4 in quinoline opls_616 1.00800 ; H5 in quinoline opls_617 1.00800 ; H6 in quinoline opls_618 1.00800 ; H7 in quinoline opls_619 1.00800 ; H8 in quinoline opls_620 14.00670 ; N1 in purine opls_621 12.01100 ; C2 in purine opls_622 14.00670 ; N3 in purine opls_623 12.01100 ; C4 in purine opls_624 12.01100 ; C5 in purine opls_625 12.01100 ; C6 in purine opls_626 14.00670 ; N7 in purine opls_627 12.01100 ; C8 in purine opls_628 14.00670 ; N9 in purine opls_629 1.00800 ; H2 in purine opls_630 1.00800 ; H6 in purine opls_631 1.00800 ; H8 in purine opls_632 1.00800 ; H9 in purine opls_633 32.06000 ; S in thiazole opls_634 12.01100 ; C2 in thiazole opls_635 14.00670 ; N in thiazole opls_636 12.01100 ; C4 in thiazole opls_637 12.01100 ; C5 in thiazole opls_638 1.00800 ; H2 in thiazole opls_639 1.00800 ; H4 in thiazole opls_640 1.00800 ; H5 in thiazole opls_641 14.00670 ; N in 1,3,5-triazine opls_642 12.01100 ; C in 1,3,5-triazine opls_643 1.00800 ; H in 1,3,5-triazine opls_644 12.01100 ; C5 in serotonin opls_645 12.01100 ; C on C3 in serotonin opls_646 14.00670 ; N1,N10 in 1,10-phenanthroline opls_647 12.01100 ; C2,C9 in 1,10-phenanthroline opls_648 12.01100 ; C3,C8 in 1,10-phenanthroline opls_649 12.01100 ; C4,C7 in 1,10-phenanthroline opls_650 12.01100 ; C12,C14 in 1,10-phenanthroline opls_651 12.01100 ; C11,C13 in 1,10-phenanthroline opls_652 12.01100 ; C5 in 1,10-phenanthroline opls_653 1.00800 ; H2,H9 in 1,10-phenanthroline opls_654 1.00800 ; H3,H8 in 1,10-phenanthroline opls_655 1.00800 ; H4,H7 in 1,10-phenanthroline opls_656 1.00800 ; H5,H6 in 1,10-phenanthroline opls_670 12.01100 ; CH3, 2-methyl pyridine opls_671 12.01100 ; CH2, 2-ethyl pyridine opls_672 12.01100 ; CH3, 3-methyl pyridazine opls_673 12.01100 ; CH2, 3-ethyl pyridazine opls_674 12.01100 ; CH3, 4-methyl pyrimidine opls_675 12.01100 ; CH2, 4-ethyl pyrimidine opls_676 12.01100 ; CH3, 2-methyl pyrazine opls_677 12.01100 ; CH2, 2-ethyl pyrazine opls_678 12.01100 ; CH3, 2-methyl pyrrole opls_679 12.01100 ; CH2, 2-ethyl pyrrole opls_680 12.01100 ; CH3, 2-methyl furan opls_681 12.01100 ; CH2, 2-ethyl furan opls_697 0.00000 ; Ac+3 Actinide params - opls_698 0.00000 ; Th+4 opls_699 0.00000 ; Am+3 F. van Veggel opls_700 12.01100 ; C+ in t-butyl+ B3LYP/6-31G* opls_701 12.01100 ; C in t-butyl+ charges opls_702 1.00800 ; H in t-butyl+ opls_703 0.00000 ; La+3 opls_704 0.00000 ; Nd+3 Lanthanide params - opls_705 0.00000 ; Eu+3 F. van Veggel, Chem Eur J 5, 90 (1999). opls_706 0.00000 ; Gd+3 opls_707 0.00000 ; Yb+3 see also JPC-A 104, 7659 (2000) opls_708 12.01100 ; C in Cl..CH3..Cl- TS opls_709 35.45300 ; Cl charges: JACS 117,2024 (95) opls_710 1.00800 ; H in Cl..CH3..Cl- TS opls_711 12.01100 ; CH2 C: cyclopropane opls_712 12.01100 ; CHR C: cyclopropane opls_713 12.01100 ; CR2 C: cyclopropane opls_714 12.01100 ; C in C5H5- cyclopentadienyl anion opls_715 1.00800 ; H in C5H5- cyclopentadienyl anion opls_716 12.01100 ; C in C5H5 cyclopentadienyl radical opls_717 1.00800 ; H in C5H5 cyclopentadienyl radical opls_718 12.01100 ; C(F) fluorobenzene opls_719 18.99840 ; F fluorobenzene opls_720 12.01100 ; C(F) hexafluorobenzene opls_721 18.99840 ; F hexafluorobenzene opls_722 79.90400 ; Br alkyl bromide (UA, but probably ok for AA) opls_724 12.01100 ; C(CF3) trifluoromethylbenzene opls_725 12.01100 ; CF3 trifluoromethylbenzene opls_726 18.99840 ; F trifluoromethylbenzene opls_727 12.01100 ; C(F) difluorobenzenes opls_728 18.99840 ; F difluorobenzenes opls_729 12.01100 ; C(Br) bromobenzene opls_730 79.90400 ; Br bromobenzene opls_731 12.01100 ; C(I) iodobenzene - tentative opls_732 126.90450 ; I iodobenzene - tentative opls_733 12.01100 ; all-atom C: CH, cyclopropyl benzene opls_734 32.06000 ; all-atom S: thiophenol (HS is #204) opls_735 12.01100 ; C(S) thiophenol opls_736 12.01100 ; CG of Benzamidine opls_737 12.01100 ; CD of Benzamidine opls_738 12.01100 ; CE of Benzamidine opls_739 12.01100 ; CZ of Benzamidine opls_740 1.00800 ; HD of Benzamidine opls_741 1.00800 ; HE of Benzamidine opls_742 12.01100 ; C+ of Benzamidine opls_743 14.00670 ; N-H2 of Benzamidine opls_744 1.00800 ; H1-N of Benzamidine opls_745 1.00800 ; H2-N of Benzamidine opls_746 1.00800 ; H-CG of Benzamidine opls_747 12.01100 ; CH3 in neutral MeGDN opls_748 12.01100 ; CD of neutral ARG opls_749 14.00670 ; NE of neutral ARG opls_750 14.00670 ; N1 of neutral ARG (HN=CZ) opls_751 14.00670 ; N2 of neutral ARG (H2N-CZ) opls_752 12.01100 ; CZ of neutral ARG opls_753 14.00670 ; N IN RCN nitriles opls_754 12.01100 ; C IN RCN nitriles opls_755 12.01100 ; C of CH3 in CH3CN opls_756 12.01100 ; C of CH2 in RCH2CN opls_757 12.01100 ; C of CH in R2CHCN opls_758 12.01100 ; C of C in R3CCN opls_759 1.00800 ; HC-CT-CN alpha-H in nitriles opls_760 14.00670 ; N in nitro R-NO2 opls_761 15.99940 ; O in nitro R-NO2 opls_762 12.01100 ; CT-NO2 nitromethane opls_763 1.00800 ; HC-CT-NO2 alpha-H in nitroalkanes opls_764 12.01100 ; CT-NO2 nitroethane opls_765 12.01100 ; CT-NO2 2-nitropropane opls_766 12.01100 ; CT-NO2 2-methyl-2-nitropropane opls_767 14.00670 ; N in nitro Ar-NO2 opls_768 12.01100 ; C(NO2) nitrobenzene opls_771 15.99940 ; propylene carbonate O (Luciennes param.) opls_772 12.01100 ; propylene carbonate C=O opls_773 15.99940 ; propylene carbonate OS opls_774 12.01100 ; propylene carbonate C in CH2 opls_775 12.01100 ; propylene carbonate C in CH opls_776 12.01100 ; propylene carbonate C in CH3 opls_777 1.00800 ; propylene carbonate H in CH2 opls_778 1.00800 ; propylene carbonate H in CH opls_779 1.00800 ; propylene carbonate H in CH3 opls_781 30.97376 ; phosphonium R4P+ opls_782 12.01100 ; CH3PR3+ 6-31G* CHELPG opls_783 12.01100 ; RCH2PR3+ opls_784 1.00800 ; H in CH3PR3+ opls_785 30.97376 ; P in PF6- opls_786 18.99840 ; F in PF6- opls_787 14.00670 ; N in NO3- opls_788 15.99940 ; O in NO3- opls_795 15.99940 ; O TIP4F Water opls_796 1.00800 ; H TIP4F Water opls_797 0.00000 ; M TIP4F Water opls_900 14.00670 ; N primary amines opls_901 14.00670 ; N secondary amines, aziridine N1 opls_902 14.00670 ; N tertiary amines opls_903 12.01100 ; CH3(N) primary aliphatic amines, H(C) is #911 opls_904 12.01100 ; CH3(N) secondary aliphatic amines, H(C) is #911 opls_905 12.01100 ; CH3(N) tertiary aliphatic amines, H(C) is #911 opls_906 12.01100 ; CH2(N) primary aliphatic amines, H(C) is #911 opls_906B 12.01100 ; CA in GLY-NH2 N-terminus opls_907 12.01100 ; CH2(N) secondary aliphatic amines, aziridine C2,C3H opls_908 12.01100 ; CH2(N) tertiary aliphatic amines, H(C) is #911 opls_909 1.00800 ; H(N) primary amines opls_910 1.00800 ; H(N) secondary amines opls_911 1.00800 ; H(C) for C bonded to N in amines, diamines (aziridine H2,H3) opls_912 12.01100 ; CH primary isopropyl amine opls_912B 12.01100 ; CA in NH2 N-terminus. All AA except GLY, PRO opls_913 12.01100 ; C primary t-butyl amine opls_914 12.01100 ; CH secondary isopropyl amine opls_915 12.01100 ; CH tertiary isopropyl amine opls_916 12.01100 ; C(NH2) aniline opls_917 12.01100 ; C(NH2) N-methylaniline opls_918 12.01100 ; C(NH2) N,N-dimethylaniline opls_925 12.01100 ; alkyne RC%CH terminal C acetylene opls_926 1.00800 ; alkyne RC%CH terminal H opls_927 12.01100 ; alkyne RC%CH C2 R-with 2 or 3 H opls_928 12.01100 ; alkyne RC%CH C2 R-with 1 H opls_929 12.01100 ; alkyne RC%CH C2 R-with no H or R=Phenyl opls_930 1.00800 ; alkyne RC%CH H on C3 (for C3 use #135-#139) opls_931 12.01100 ; alkyne RC%CR opls_940 14.00670 ; N (R3NH+) opls_941 1.00800 ; H (R3NH+) opls_942 12.01100 ; C in CH3NHR2+ opls_943 12.01100 ; C in RCH2NHR2+ opls_944 12.01100 ; C in R2CHNHR2+ opls_945 12.01100 ; C in R3CNHR2+ opls_950 1.00800 ; glycine zwit. 6-31G* CHELPG charges opls_951 12.01100 ; glycine zwit. 6-31G* CHELPG charges opls_952 12.01100 ; glycine zwit. 6-31G* CHELPG charges opls_953 14.00670 ; glycine zwit. 6-31G* CHELPG charges opls_954 15.99940 ; glycine zwit. 6-31G* CHELPG charges opls_955 1.00800 ; glycine zwit. 6-31G* CHELPG charges opls_956 18.99840 ; F in monoalkyl fluorides (tentative) opls_957 12.01100 ; RCH2F in monoalkyl fluorides (tentative) opls_958 1.00800 ; H in RCHF in monoalkyl fluorides (tentative) opls_959 12.01100 ; R2CHF in monoalkyl fluorides (tentative) opls_960 12.01100 ; R3CF in monoalkyl fluorides (tentative) opls_961 12.01100 ; CF3 perfluoroalkanes opls_962 12.01100 ; CF2 perfluoroalkanes opls_963 12.01100 ; CF perfluoroalkanes opls_964 12.01100 ; CF4 opls_965 18.99840 ; F: perfluoroalkanes MNH3 0.0 ; Dummy mass in rigid tetraedrical NH3 group MNH2 0.0 ; Dummy mass in rigid umbrella-shaped NH2 group MCH3A 0.0 ; Dummy mass in rigid tetraedrical CH3 group MCH3B 0.0 ; Dummy mass in rigid tetraedrical CH3 group MW 0.0 ; Dummy mass in rigid tyrosine rings DUM 0.0 ; Dummy mass in TIP4P etc. ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins we have added them. Cu2+ 63.546 ; Copper. See Inorg. Chem. 40, 5223 (2001). Fe2+ 55.847 ; Iron Zn2+ 65.370 ; Zinc Ar 39.948 ; Argon ; Added by DvdS 05/2005 copied from GROMACS force field. SI 28.080 ; Silicium in Glass etc.
Даны 5 файлов с разными параметрами контроля температуры:
be.mdp - метод Берендсена для контроля температуры.
vr.mdp - метод "Velocity rescale" для контроля температуры.
nh.mdp - метод Нуза-Хувера для контроля температуры.
an.mdp - метод Андерсена для контроля температуры.
sd.mdp - метод стохастической молекулярной динамики.
Рассмотрим их более подробно. Будем искать, в чем их различия. Для начала я скачала эти файлы в директорию практикума.
In [23]:
%%bash
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
wget http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/etane.gro
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 399
Saving to: `etane.gro.1'
0K 100% 49.1M=0s
2017-05-29 02:45:29 (49.1 MB/s) - `etane.gro.1' saved [399/399]
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/be.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1356 (1.3K)
Saving to: `be.mdp.1'
0K . 100% 127M=0s
2017-05-29 02:45:29 (127 MB/s) - `be.mdp.1' saved [1356/1356]
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/vr.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1427 (1.4K)
Saving to: `vr.mdp.1'
0K . 100% 197M=0s
2017-05-29 02:45:29 (197 MB/s) - `vr.mdp.1' saved [1427/1427]
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/nh.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1429 (1.4K)
Saving to: `nh.mdp.1'
0K . 100% 143M=0s
2017-05-29 02:45:29 (143 MB/s) - `nh.mdp.1' saved [1429/1429]
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/an.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1426 (1.4K)
Saving to: `an.mdp.1'
0K . 100% 139M=0s
2017-05-29 02:45:29 (139 MB/s) - `an.mdp.1' saved [1426/1426]
--2017-05-29 02:45:29-- http://kodomo.fbb.msu.ru/FBB/year_08/term6/sd.mdp
Resolving kodomo.fbb.msu.ru... 192.168.180.1
Connecting to kodomo.fbb.msu.ru|192.168.180.1|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1441 (1.4K)
Saving to: `sd.mdp.1'
0K . 100% 155M=0s
2017-05-29 02:45:29 (155 MB/s) - `sd.mdp.1' saved [1441/1441]
Запустим grompp, используя 5 файлов с разными параметрами контроля температуры. Получим 5 .tpr файлов.
In [27]:
import subprocess
for filename in ['be','vr','nh','an','sd']:
cmd = 'grompp -f %s.mdp -c etane.gro -p et.top -o et_%s.tpr >& log.grompp' %(filename,filename)
subprocess.call(cmd,shell=True)
# где i: be,vr,nh,an,sd см. выше список mdp файлов
Теперь для каждого из них запустим mdrun.
In [29]:
for filename in ['be','vr','nh','an','sd']:
cmd = 'mdrun -deffnm et_%s.tpr -v -nt 1' %filename
subprocess.call(cmd,shell=True)
Теперь переходим к анализу результатов. Начнем с визуального анализа. Для каждой из 5 систем проведем конвертацию в pdb и просмотрим в PyMol.
smooth в PyMol дает возможность смотреть на более плавное движение молекул.
et_an еле колеблется;
et_be, et_nh, et_vr довольно похожи по характеру движения, движутся по кругу в одной плоскости и быстро вращаются вокруг С-С связи;
et_sd быстро и беспорядочно движется во всех направлениях, улетая от начального положения дальше всех.
In [34]:
for filename in ['be','vr','nh','an','sd']:
cmd = 'echo 0 | trjconv -f et_%s.tpr.trr -s et_%s.tpr -o et_%s.pdb >& log.trjconv' %(filename,filename,filename)
subprocess.call(cmd,shell=True)
Сравним потенциальную энергию связи и кинетическую энергию для каждой из 5 систем.
In [42]:
for filename in ['be','vr','nh','an','sd']:
cmd1 = 'echo 10 | g_energy -f et_%s.tpr.edr -o et_%s_pot_en.xvg -xvg none >& log.g_energy' %(filename,filename)
cmd2 = 'echo 11 | g_energy -f et_%s.tpr.edr -o et_%s_kin_en.xvg -xvg none >& log.g_energy' %(filename,filename)
subprocess.call(cmd1,shell=True)
subprocess.call(cmd2,shell=True)
In [45]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['be','vr','nh','an','sd']:
a= np.loadtxt('et_%s_pot_en.xvg' % filename)
b= np.loadtxt('et_%s_kin_en.xvg' % filename)
t1=a[:,0]
y1=a[:,1]
t2=b[:,0]
y2=b[:,1]
plt.plot(t1, y1, "b-", t2, y2, "r-" )
red_patch = mpatches.Patch(color='red', label='Kinetic')
blue_patch = mpatches.Patch(color='blue', label='Potential')
plt.legend(handles=[red_patch,blue_patch])
plt.title('Energies of %s system' % filename)
plt.show()
По форме распределение энергий для be отличается от всех остальных: амплитуда колебаний значений уменьшается со временем. У остальных методов она остается примерно постоянной. Различаются только абсолютные значения амплитуды: самые маленькие у an, самые большие у nh.
Рассмотрим распределение длины связи С-С за время моделирования. Сначала создадим индекс файл с одной связью b.ndx. Это индексы атомов, образующих связь, - в нашем случае 1 и 2. Затем построим распределения длин.
In [46]:
import subprocess
for filename in ['be','vr','nh','an','sd']:
cmd = 'g_bond -f et_%s.tpr.trr -s et_%s.tpr -o bond_%s.xvg -n b.ndx -xvg none' % (filename,filename,filename)
subprocess.call(cmd,shell=True)
In [47]:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
for filename in ['be','vr','nh','an','sd']:
a= np.loadtxt('bond_%s.xvg' % filename)
t1=a[:,0]
y1=a[:,1]
width = 0.0001 #эмпирически
plt.bar(t1,y1,width, color="blue")
plt.title('Length of C-C bond in %s system' % filename)
plt.show()
На распределение Максвелла-Больцмана похожи распределения длин С-С связей в системах be и nh. У них есть пик при длине 0,153 - это соответствует средней длине С-С связи в этане. У распределений vr и an это значение - локальный минимум, что очень странно. Распределение be симметричное, в то время как у nh правый хвост длиннее левого. Значит, распределение nh больше всего похоже на распределение Максвелла-Больцмана.
Для каждого из алгоритмов подсчитаем время работы. В принципе, для этого можно использовать функцию time или /usr/bin/time из bash. Но время работы скрипта прописано в тексте выдачи GROMACS.
Тогда нужно создать отдельные скрипты для каждого алгоритма.
In [49]:
import subprocess
for filename in ['be','vr','nh','an','sd']:
cmd1 = 'grompp -f %s.mdp -c etane.gro -p et.top -o et_%s.tpr >& log.grompp' %(filename,filename)
cmd2 = 'mdrun -deffnm et_%s.tpr -v -nt 1' %filename
output_file = open(filename+'.sh','w')
output_file.writelines('\n'.join([cmd1,cmd2]))
output_file.close()
In [50]:
%%bash
chmod +x *.sh
./be.sh
./vr.sh
./nh.sh
./an.sh
./sd.sh
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_be.tpr Input Run input file: tpr tpb tpa
-o et_be.tpr.trr Output Full precision trajectory: trr trj cpt
-x et_be.tpr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_be.tpr.cpt Input, Opt. Checkpoint file
-cpo et_be.tpr.cpt Output, Opt. Checkpoint file
-c et_be.tpr.gro Output Structure file: gro g96 pdb etc.
-e et_be.tpr.edr Output Energy file
-g et_be.tpr.log Output Log file
-dhdl et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-field et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-table et_be.tpr.xvg Input, Opt. xvgr/xmgr file
-tablep et_be.tpr.xvg Input, Opt. xvgr/xmgr file
-tableb et_be.tpr.xvg Input, Opt. xvgr/xmgr file
-rerun et_be.tpr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-tpid et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-ei et_be.tpr.edi Input, Opt. ED sampling input
-eo et_be.tpr.edo Output, Opt. ED sampling output
-j et_be.tpr.gct Input, Opt. General coupling stuff
-jo et_be.tpr.gct Output, Opt. General coupling stuff
-ffout et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-devout et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-runav et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-px et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-pf et_be.tpr.xvg Output, Opt. xvgr/xmgr file
-mtx et_be.tpr.mtx Output, Opt. Hessian matrix
-dn et_be.tpr.ndx Output, Opt. Index file
-multidir et_be.tpr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string et_be.tpr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up et_be.tpr.log to ./#et_be.tpr.log.3#
Getting Loaded...
Reading file et_be.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_be.tpr.trr to ./#et_be.tpr.trr.3#
Back Off! I just backed up et_be.tpr.edr to ./#et_be.tpr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_be.tpr.gro to ./#et_be.tpr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.740 3.951 94.7
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 364.963 5775.425 0.004
gcq#36: "All Work and No Play Makes Jack a Dull Boy" (The Shining)
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_vr.tpr Input Run input file: tpr tpb tpa
-o et_vr.tpr.trr Output Full precision trajectory: trr trj cpt
-x et_vr.tpr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_vr.tpr.cpt Input, Opt. Checkpoint file
-cpo et_vr.tpr.cpt Output, Opt. Checkpoint file
-c et_vr.tpr.gro Output Structure file: gro g96 pdb etc.
-e et_vr.tpr.edr Output Energy file
-g et_vr.tpr.log Output Log file
-dhdl et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-field et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-table et_vr.tpr.xvg Input, Opt. xvgr/xmgr file
-tablep et_vr.tpr.xvg Input, Opt. xvgr/xmgr file
-tableb et_vr.tpr.xvg Input, Opt. xvgr/xmgr file
-rerun et_vr.tpr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-tpid et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-ei et_vr.tpr.edi Input, Opt. ED sampling input
-eo et_vr.tpr.edo Output, Opt. ED sampling output
-j et_vr.tpr.gct Input, Opt. General coupling stuff
-jo et_vr.tpr.gct Output, Opt. General coupling stuff
-ffout et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-devout et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-runav et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-px et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-pf et_vr.tpr.xvg Output, Opt. xvgr/xmgr file
-mtx et_vr.tpr.mtx Output, Opt. Hessian matrix
-dn et_vr.tpr.ndx Output, Opt. Index file
-multidir et_vr.tpr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string et_vr.tpr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up et_vr.tpr.log to ./#et_vr.tpr.log.3#
Getting Loaded...
Reading file et_vr.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_vr.tpr.trr to ./#et_vr.tpr.trr.3#
Back Off! I just backed up et_vr.tpr.edr to ./#et_vr.tpr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_vr.tpr.gro to ./#et_vr.tpr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.840 4.099 93.7
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 355.393 5625.023 0.004
gcq#130: "Everybody Wants to Be Naked and Famous" (Tricky)
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_nh.tpr Input Run input file: tpr tpb tpa
-o et_nh.tpr.trr Output Full precision trajectory: trr trj cpt
-x et_nh.tpr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_nh.tpr.cpt Input, Opt. Checkpoint file
-cpo et_nh.tpr.cpt Output, Opt. Checkpoint file
-c et_nh.tpr.gro Output Structure file: gro g96 pdb etc.
-e et_nh.tpr.edr Output Energy file
-g et_nh.tpr.log Output Log file
-dhdl et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-field et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-table et_nh.tpr.xvg Input, Opt. xvgr/xmgr file
-tablep et_nh.tpr.xvg Input, Opt. xvgr/xmgr file
-tableb et_nh.tpr.xvg Input, Opt. xvgr/xmgr file
-rerun et_nh.tpr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-tpid et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-ei et_nh.tpr.edi Input, Opt. ED sampling input
-eo et_nh.tpr.edo Output, Opt. ED sampling output
-j et_nh.tpr.gct Input, Opt. General coupling stuff
-jo et_nh.tpr.gct Output, Opt. General coupling stuff
-ffout et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-devout et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-runav et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-px et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-pf et_nh.tpr.xvg Output, Opt. xvgr/xmgr file
-mtx et_nh.tpr.mtx Output, Opt. Hessian matrix
-dn et_nh.tpr.ndx Output, Opt. Index file
-multidir et_nh.tpr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string et_nh.tpr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up et_nh.tpr.log to ./#et_nh.tpr.log.3#
Getting Loaded...
Reading file et_nh.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_nh.tpr.trr to ./#et_nh.tpr.trr.3#
Back Off! I just backed up et_nh.tpr.edr to ./#et_nh.tpr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_nh.tpr.gro to ./#et_nh.tpr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.840 4.049 94.8
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 355.188 5625.023 0.004
gcq#338: "Making merry out of nothing, like in refugee camp" (Gogol Bordello)
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in Calculating Stuff
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_an.tpr Input Run input file: tpr tpb tpa
-o et_an.tpr.trr Output Full precision trajectory: trr trj cpt
-x et_an.tpr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_an.tpr.cpt Input, Opt. Checkpoint file
-cpo et_an.tpr.cpt Output, Opt. Checkpoint file
-c et_an.tpr.gro Output Structure file: gro g96 pdb etc.
-e et_an.tpr.edr Output Energy file
-g et_an.tpr.log Output Log file
-dhdl et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-field et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-table et_an.tpr.xvg Input, Opt. xvgr/xmgr file
-tablep et_an.tpr.xvg Input, Opt. xvgr/xmgr file
-tableb et_an.tpr.xvg Input, Opt. xvgr/xmgr file
-rerun et_an.tpr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-tpid et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-ei et_an.tpr.edi Input, Opt. ED sampling input
-eo et_an.tpr.edo Output, Opt. ED sampling output
-j et_an.tpr.gct Input, Opt. General coupling stuff
-jo et_an.tpr.gct Output, Opt. General coupling stuff
-ffout et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-devout et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-runav et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-px et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-pf et_an.tpr.xvg Output, Opt. xvgr/xmgr file
-mtx et_an.tpr.mtx Output, Opt. Hessian matrix
-dn et_an.tpr.ndx Output, Opt. Index file
-multidir et_an.tpr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string et_an.tpr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up et_an.tpr.log to ./#et_an.tpr.log.3#
Getting Loaded...
Reading file et_an.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_an.tpr.trr to ./#et_an.tpr.trr.3#
Back Off! I just backed up et_an.tpr.edr to ./#et_an.tpr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_an.tpr.gro to ./#et_an.tpr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 3.720 3.942 94.4
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 367.509 5806.475 0.004
gcq#66: "Give a Man a Fish" (Arrested Development)
:-) G R O M A C S (-:
Great Red Owns Many ACres of Sand
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s et_sd.tpr Input Run input file: tpr tpb tpa
-o et_sd.tpr.trr Output Full precision trajectory: trr trj cpt
-x et_sd.tpr.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi et_sd.tpr.cpt Input, Opt. Checkpoint file
-cpo et_sd.tpr.cpt Output, Opt. Checkpoint file
-c et_sd.tpr.gro Output Structure file: gro g96 pdb etc.
-e et_sd.tpr.edr Output Energy file
-g et_sd.tpr.log Output Log file
-dhdl et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-field et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-table et_sd.tpr.xvg Input, Opt. xvgr/xmgr file
-tablep et_sd.tpr.xvg Input, Opt. xvgr/xmgr file
-tableb et_sd.tpr.xvg Input, Opt. xvgr/xmgr file
-rerun et_sd.tpr.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-tpid et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-ei et_sd.tpr.edi Input, Opt. ED sampling input
-eo et_sd.tpr.edo Output, Opt. ED sampling output
-j et_sd.tpr.gct Input, Opt. General coupling stuff
-jo et_sd.tpr.gct Output, Opt. General coupling stuff
-ffout et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-devout et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-runav et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-px et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-pf et_sd.tpr.xvg Output, Opt. xvgr/xmgr file
-mtx et_sd.tpr.mtx Output, Opt. Hessian matrix
-dn et_sd.tpr.ndx Output, Opt. Index file
-multidir et_sd.tpr Input, Opt., Mult. Run directory
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string et_sd.tpr Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-nt int 1 Number of threads to start (0 is guess)
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up et_sd.tpr.log to ./#et_sd.tpr.log.3#
Getting Loaded...
Reading file et_sd.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up et_sd.tpr.trr to ./#et_sd.tpr.trr.3#
Back Off! I just backed up et_sd.tpr.edr to ./#et_sd.tpr.edr.3#
starting mdrun 'first one'
250000 steps, 250.0 ps.
step 249900, remaining runtime: 0 s
Writing final coordinates.
Back Off! I just backed up et_sd.tpr.gro to ./#et_sd.tpr.gro.3#
step 250000, remaining runtime: 0 s
NODE (s) Real (s) (%)
Time: 4.330 4.580 94.5
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 329.441 4988.473 0.005
gcq#275: "Does All This Money Really Have To Go To Charity ?" (Rick)
В таблице данные по времени NODE из output GROMACS.
Стоит отметить, что, так как это не первый запуск grompp и mdrun, то требовалось еще переименовать предыдущие версии файлов. Но это влияет на абсолютные, а не на относительные значения.
Быстрее всех сработал an, а медленнее всех - sd. Это коррелирует с визуальным анализом движения молекул: чем больше изменяются координаты молекулы в пространстве, тем больше времени занимают расчеты.
Algorithm | Time, s |
|---|---|
be | 3.740 |
vr | 3.840 |
nh | 3.840 |
an | 3.720 |
sd | 4.330 |