Изучение работы методов контроля температуры в молекулярной динамике

Изучим, как реализован контроль температуры в молекулярной динамике на примере GROMACS. Объект исследования это одна молекула этана. Для начала подготовим файл координат и файл топологии.

In [1]:
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
import os
import io
import base64
from IPython.display import HTML
import matplotlib.pyplot as plt
In [3]:
# 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[3]:
0
In [12]:
# и придумаем циклы 
## связи
print('Связи')
bonds = m3d.GetBonds()
for i,b in enumerate(bonds):
    print b.GetBeginAtomIdx() + 1, b.GetEndAtomIdx() + 1, '1'

## углы  
print('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'
            
## dihedrals 
print('Торсионные 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'
                

Связи
1 2 1
1 3 1
1 4 1
1 5 1
2 6 1
2 7 1
2 8 1
Углы
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
Торсионные углы
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
In [9]:
%%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.

Отметим нужные строки:

opls_139 12.01100 ; alkane C
opls_140 1.00800 ; alkane H.

И создадим файл et.top.

In [13]:
for i in ['be', 'vr', 'nh', 'an', 'sd']:
    # построим входные файлы для молекулярно-динамического движка
    os.system('grompp -f %s.mdp -c et.gro -p et.top -o et_%s.tpr' % (i, i))
    os.system('mdrun -deffnm et_%s -v -nt 1' % i)
    # проведем конвертацию в pdb
    os.system('trjconv -f et_%s.trr -s et_%s.tpr -o et_%s.pdb' % (i, i, i))

Визуальный анализ

In [2]:
for i, name in zip(['be', 'vr', 'nh', 'an', 'sd'], ['метод Берендсена для контроля температуры',
                                              'метод "Velocity rescale" для контроля температуры',
                                              'метод Нуза-Хувера для контроля температуры',
                                              'метод Андерсена для контроля температуры',
                                              'метод стохастической молекулярной динамики']):
    print(name)
    video = io.open('et_%s.mp4' % i, 'r+b').read()
    encoded = base64.b64encode(video)
    display(HTML(data='''<video alt="test" controls>
                    <source src="data:video/mp4;base64,{0}" type="video/mp4" />
                 </video>'''.format(encoded.decode('ascii'))))

метод Берендсена для контроля температуры

метод "Velocity rescale" для контроля температуры

метод Нуза-Хувера для контроля температуры

метод Андерсена для контроля температуры

метод стохастической молекулярной динамики

При использовании метода Берендсена молекула этана начинает слишком быстро крутиться, что выглядит странно. При методе "Velocity rescale" наблюдаются небольшие колебания длины С-С связи и можно различить заслоненную и заторможенную конформацию, но скорость вращения очень высокая. При методе Нуза-Хувера практически не происходит изменение длины связи C-C и видна заслоненная и заторможенная конформация. При методе Андерсена в молекуле происходят только колебательные движения. При применении метода стохастической молекулярной динамики сложно отследить изменения в длине связи и во вращательных движениях, потому что молекула очень быстро прыгает по экрану.

In [32]:
for i in ['be', 'vr', 'nh', 'an', 'sd']:
#     Сравним потенциальную энергию и кинетическую энергию для каждой из 5 систем.
    os.system('echo 10 | g_energy -f et_%s.edr -o et_%s_potential.xvg -xvg none' % (i, i))
    os.system('echo 11 | g_energy -f et_%s.edr -o et_%s_kinetic.xvg -xvg none' % (i, i))
In [3]:
for i, name in zip(['be', 'vr', 'nh', 'an', 'sd'], ['методу Берендсена для контроля температуры',
                                              'методу "Velocity rescale" для контроля температуры',
                                              'методу Нуза-Хувера для контроля температуры',
                                              'методу Андерсена для контроля температуры',
                                              'методу стохастической молекулярной динамики']):
    print('Энергия в системе по %s' % name)  
    potential = np.loadtxt('et_%s_potential.xvg' % i)
    kinetic = np.loadtxt('et_%s_kinetic.xvg' % i)
    t_pot = potential[:,0]
    t_kin = kinetic[:,0]
    y_pot = potential[:,1]
    y_kin = kinetic[:,1]
    plt.plot(t_pot, y_pot, label = 'Potential energy', c = 'orangered', linewidth=1.5, zorder = 100)
    plt.plot(t_kin, y_kin, label = 'Kinetic energy', c = 'lightslategray', linewidth=1.5, zorder = 100)
    plt.legend()
    plt.show()

Энергия в системе по методу Берендсена для контроля температуры

Энергия в системе по методу "Velocity rescale" для контроля температуры

Энергия в системе по методу Нуза-Хувера для контроля температуры

Энергия в системе по методу Андерсена для контроля температуры

Энергия в системе по методу стохастической молекулярной динамики

Распеределения кинетической и потенциальной энергии являются практически идентичными.

In [55]:
for i in ['be', 'vr', 'nh', 'an', 'sd']:
    os.system('echo 0 | g_bond -f et_%s.trr -s et_%s.tpr -o bond_%s.xvg -n b.ndx -xvg none' % (i, i, i))
In [7]:
for i, name in zip(['be', 'vr', 'nh', 'an', 'sd'], ['методу Берендсена для контроля температуры',
                                              'методу "Velocity rescale" для контроля температуры',
                                              'методу Нуза-Хувера для контроля температуры',
                                              'методу Андерсена для контроля температуры',
                                              'методу стохастической молекулярной динамики']):
    print('Длина C-C связи в системе по %s' % name)  
    bond = np.loadtxt('bond_%s.xvg' % i)
    x = bond[:,0]
    y = bond[:,1]
    plt.bar(x, y, width = 0.001, label = 'C-C bond length', color = 'lightslategray')
    plt.legend()
    plt.xlim(0.135, 0.17)
    plt.show()

Длина C-C связи в системе по методу Берендсена для контроля температуры

Длина C-C связи в системе по методу "Velocity rescale" для контроля температуры

Длина C-C связи в системе по методу Нуза-Хувера для контроля температуры

Длина C-C связи в системе по методу Андерсена для контроля температуры

Длина C-C связи в системе по методу стохастической молекулярной динамики

Распределению Больцмана наиболее соответствуют распределения длин С-С связей в системах по методу по методу "Velocity rescale" и по методу стохастической молекулярной динамики, однако при последнем методе наблюдается хаотичное движение молекулы. Поэтому я считаю метод Velocity rescale самым правдоподобным.

In [61]:
import time
for i in ["be","vr","nh","an","sd"]:
    # построим входные файлы для молекулярно-динамического движка
    os.system('grompp -f %s.mdp -c et.gro -p et.top -o et_%s.tpr' % (i, i))
    start_time = time.time()
    os.system('mdrun -deffnm et_%s -v -nt 1' % i)
    print("--- %s seconds for %s ---" % ((time.time() - start_time), i))

--- 4.08796906471 seconds for be ---
--- 4.20370292664 seconds for vr ---
--- 4.22787308693 seconds for nh ---
--- 4.08230900764 seconds for an ---
--- 4.71216201782 seconds for sd ---