In [2]:
!cp -r /home/preps/golovin/progs/share/gromacs/top/gmx.ff ./
In [3]:
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/dppc.itp'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/lipid.itp'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/dppc.gro'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/b.top'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/em.mdp'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/pr.mdp'
!wget 'http://kodomo.cmm.msu.ru/~golovin/bilayer/md.mdp'
--2026-04-11 17:48:07-- http://kodomo.cmm.msu.ru/~golovin/bilayer/dppc.itp Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/dppc.itp [following] --2026-04-11 17:48:07-- https://kodomo.fbb.msu.ru/~golovin/bilayer/dppc.itp Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 12772 (12K) [application/vnd.shana.informed.formtemplate] Saving to: ‘dppc.itp’ dppc.itp 100%[===================>] 12.47K --.-KB/s in 0s 2026-04-11 17:48:07 (122 MB/s) - ‘dppc.itp’ saved [12772/12772] --2026-04-11 17:48:07-- http://kodomo.cmm.msu.ru/~golovin/bilayer/lipid.itp Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/lipid.itp [following] --2026-04-11 17:48:07-- https://kodomo.fbb.msu.ru/~golovin/bilayer/lipid.itp Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 34337 (34K) [application/vnd.shana.informed.formtemplate] Saving to: ‘lipid.itp’ lipid.itp 100%[===================>] 33.53K --.-KB/s in 0s 2026-04-11 17:48:07 (156 MB/s) - ‘lipid.itp’ saved [34337/34337] --2026-04-11 17:48:07-- http://kodomo.cmm.msu.ru/~golovin/bilayer/dppc.gro Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/dppc.gro [following] --2026-04-11 17:48:07-- https://kodomo.fbb.msu.ru/~golovin/bilayer/dppc.gro Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2329 (2.3K) Saving to: ‘dppc.gro’ dppc.gro 100%[===================>] 2.27K --.-KB/s in 0s 2026-04-11 17:48:07 (95.6 MB/s) - ‘dppc.gro’ saved [2329/2329] --2026-04-11 17:48:08-- http://kodomo.cmm.msu.ru/~golovin/bilayer/b.top Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/b.top [following] --2026-04-11 17:48:08-- https://kodomo.fbb.msu.ru/~golovin/bilayer/b.top Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 541 Saving to: ‘b.top’ b.top 100%[===================>] 541 --.-KB/s in 0s 2026-04-11 17:48:08 (15.2 MB/s) - ‘b.top’ saved [541/541] --2026-04-11 17:48:08-- http://kodomo.cmm.msu.ru/~golovin/bilayer/em.mdp Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/em.mdp [following] --2026-04-11 17:48:08-- https://kodomo.fbb.msu.ru/~golovin/bilayer/em.mdp Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1088 (1.1K) Saving to: ‘em.mdp’ em.mdp 100%[===================>] 1.06K --.-KB/s in 0s 2026-04-11 17:48:08 (42.9 MB/s) - ‘em.mdp’ saved [1088/1088] --2026-04-11 17:48:08-- http://kodomo.cmm.msu.ru/~golovin/bilayer/pr.mdp Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/pr.mdp [following] --2026-04-11 17:48:08-- https://kodomo.fbb.msu.ru/~golovin/bilayer/pr.mdp Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1164 (1.1K) Saving to: ‘pr.mdp’ pr.mdp 100%[===================>] 1.14K --.-KB/s in 0s 2026-04-11 17:48:08 (44.7 MB/s) - ‘pr.mdp’ saved [1164/1164] --2026-04-11 17:48:08-- http://kodomo.cmm.msu.ru/~golovin/bilayer/md.mdp Resolving kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)... 93.180.63.127 Connecting to kodomo.cmm.msu.ru (kodomo.cmm.msu.ru)|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://kodomo.fbb.msu.ru/~golovin/bilayer/md.mdp [following] --2026-04-11 17:48:08-- https://kodomo.fbb.msu.ru/~golovin/bilayer/md.mdp Resolving kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)... 192.168.180.1 Connecting to kodomo.fbb.msu.ru (kodomo.fbb.msu.ru)|192.168.180.1|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1276 (1.2K) Saving to: ‘md.mdp’ md.mdp 100%[===================>] 1.25K --.-KB/s in 0s 2026-04-11 17:48:08 (52.4 MB/s) - ‘md.mdp’ saved [1276/1276]
In [ ]:
# Моделирование самосборки липидного бислоя
In [ ]:
#Мы скачали файлы:
#дополнительной топологии для липида DPPC, dppc.itp.
#параметры для липидов lipid.itp.
#координаты одного липида dppc.gro.
#Файл-заготовка тополгии системы b.top.
#файл праметров для минимизации энергии em.mdp.
#файл праметров для "утряски" воды pr.mdp pr.mdp.
#файл праметров для молекулярной динамики md.mdp.
#фалы силового поля (gmx.ff)
In [4]:
# На основе одного липида созадим ячейку с 64 липидами.
!gmx genconf -f dppc.gro -o b_64.gro -nbox 4 4 4
:-) GROMACS - gmx genconf, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr8 Command line: gmx genconf -f dppc.gro -o b_64.gro -nbox 4 4 4 GROMACS reminds you: "Chemical gases filling lungs of little ones" (Black Eyed Peas)
In [5]:
#С помощью editconf преобразуем dppc.gro и b_64.gro в pdb файлы и посмотрим их в pymol
!gmx editconf -f dppc.gro -o dppc.pdb
!gmx editconf -f b_64.gro -o b_64.pdb
:-) GROMACS - gmx editconf, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr8
Command line:
gmx editconf -f dppc.gro -o dppc.pdb
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 50 atoms
Volume: 1.5477 nm^3, corresponds to roughly 600 electrons
No velocities found
GROMACS reminds you: "It is an unfortunate fact that when you raise the question of the reliability of many simulations you are often told about how much manpower went into it, how large & fast the computer is, how important the problem is, and such things, which are completely irrelevant to the question that was asked." (Richard Hamming)
:-) GROMACS - gmx editconf, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr8
Command line:
gmx editconf -f b_64.gro -o b_64.pdb
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 3200 atoms
Volume: 99.0529 nm^3, corresponds to roughly 44500 electrons
No velocities found
GROMACS reminds you: "It is an unfortunate fact that when you raise the question of the reliability of many simulations you are often told about how much manpower went into it, how large & fast the computer is, how important the problem is, and such things, which are completely irrelevant to the question that was asked." (Richard Hamming)
In [6]:
from IPython.display import Image
In [7]:
Image(filename='dppc.png')
Out[7]:
In [8]:
Image(filename='b_64.png')
Out[8]:
In [9]:
#В текстовом редакторе в файле b.top установим количество липидов в системе = 64
#; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion
#; alm.itp can be made in a straightforward manner with pdb2gmx, starting
#; with a pdb file of alamethicin.
#; make sure lipid.itp, popc.itp and alm.itp are in a location where
#; grompp can find them (GMXLIB, current directory, or directory given in
#; the .mdp file with the include option.
#include "gmx.ff/forcefield.itp"
#include "lipid.itp"
#include "dppc.itp"
#include "gmx.ff/spc.itp"
#[ system ]
#; name
#bilayer in water
#[ molecules ]
#; name number
#DPPC 64
In [10]:
#Сделаем небольшой отступ в ячейке от липидов, что бы добавить примерно 2500 молекул воды.
!gmx editconf -f b_64.gro -o b_ec -d 0.5
:-) GROMACS - gmx editconf, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx editconf -f b_64.gro -o b_ec -d 0.5
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 3200 atoms
Volume: 99.0529 nm^3, corresponds to roughly 44500 electrons
No velocities found
system size : 5.260 3.443 4.778 (nm)
center : 2.730 1.822 2.490 (nm)
box vectors : 5.460 3.643 4.979 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 99.05 (nm^3)
shift : 0.400 0.400 0.399 (nm)
new center : 3.130 2.222 2.889 (nm)
new box vectors : 6.260 4.443 5.778 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 160.70 (nm^3)
WARNING: No boxtype specified - distance condition applied in each dimension.
If the molecule rotates the actual distance will be smaller. You might want
to use a cubic box instead, or why not try a dodecahedron today?
GROMACS reminds you: "Nothing shocks me. I'm a scientist." (Harrison Ford as Indiana Jones)
In [11]:
#Проведём оптимизацию геометрии системы, что бы удалить "плохие" контакты молекул.
!gmx grompp -f em -c b_ec -p b -o b_em -maxwarn 2
:-) GROMACS - gmx grompp, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx grompp -f em -c b_ec -p b -o b_em -maxwarn 2
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 1275032559
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'DPPC'
WARNING 1 [file b.top, line 20]:
The following macros were defined in the 'define' mdp field with the -D
prefix, but were not used in the topology:
FLEX_SPC
If you haven't made a spelling error, either use the macro you defined,
or don't define the macro
Analysing residue names:
There are: 64 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 9597.00
NOTE 2 [file em.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 79 Mb of data
There were 2 notes
There was 1 warning
GROMACS reminds you: "Hmm, It *Does* Go Well With the Chicken" (Beastie Boys)
In [12]:
!gmx mdrun -deffnm b_em -v
:-) GROMACS - gmx mdrun, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr7 Command line: gmx mdrun -deffnm b_em -v Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see log). Reading file b_em.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) Using 1 MPI thread Using 8 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. Steepest Descents: Tolerance (Fmax) = 1.00000e+00 Number of steps = 1000000 Step= 0, Dmax= 2.0e-02 nm, Epot= 4.63572e+05 Fmax= 4.37969e+05, atom= 1842 Step= 1, Dmax= 2.0e-02 nm, Epot= 6.01385e+04 Fmax= 3.57932e+04, atom= 2988 Step= 2, Dmax= 2.4e-02 nm, Epot= 1.17292e+04 Fmax= 9.52568e+03, atom= 2993 Step= 3, Dmax= 2.9e-02 nm, Epot= 4.52558e+03 Fmax= 1.50702e+04, atom= 1392 Step= 4, Dmax= 3.5e-02 nm, Epot= -9.49027e+02 Fmax= 1.36727e+04, atom= 2942 Step= 6, Dmax= 2.1e-02 nm, Epot= -1.81015e+04 Fmax= 4.05971e+03, atom= 2992 Step= 9, Dmax= 6.2e-03 nm, Epot= -2.09460e+04 Fmax= 1.84753e+03, atom= 2942 Step= 10, Dmax= 7.5e-03 nm, Epot= -2.16611e+04 Fmax= 3.76142e+03, atom= 2942 Step= 11, Dmax= 9.0e-03 nm, Epot= -2.16924e+04 Fmax= 4.34201e+03, atom= 2692 Step= 13, Dmax= 5.4e-03 nm, Epot= -2.48063e+04 Fmax= 1.92804e+03, atom= 2915 Step= 15, Dmax= 3.2e-03 nm, Epot= -2.53117e+04 Fmax= 2.21950e+03, atom= 2915 Step= 16, Dmax= 3.9e-03 nm, Epot= -2.56977e+04 Fmax= 2.62931e+03, atom= 2915 Step= 17, Dmax= 4.6e-03 nm, Epot= -2.59506e+04 Fmax= 3.30451e+03, atom= 2915 Step= 18, Dmax= 5.6e-03 nm, Epot= -2.61731e+04 Fmax= 3.72856e+03, atom= 2915 Step= 20, Dmax= 3.3e-03 nm, Epot= -2.69059e+04 Fmax= 5.67246e+02, atom= 2915 Step= 21, Dmax= 4.0e-03 nm, Epot= -2.73377e+04 Fmax= 4.23350e+03, atom= 2915 Step= 22, Dmax= 4.8e-03 nm, Epot= -2.80685e+04 Fmax= 1.90933e+03, atom= 2915 Step= 24, Dmax= 2.9e-03 nm, Epot= -2.82703e+04 Fmax= 1.74077e+03, atom= 2915 Step= 25, Dmax= 3.5e-03 nm, Epot= -2.83253e+04 Fmax= 2.67800e+03, atom= 2915 Step= 26, Dmax= 4.2e-03 nm, Epot= -2.85041e+04 Fmax= 2.59052e+03, atom= 2915 Step= 28, Dmax= 2.5e-03 nm, Epot= -2.88583e+04 Fmax= 6.09165e+02, atom= 2915 Step= 29, Dmax= 3.0e-03 nm, Epot= -2.89406e+04 Fmax= 3.08950e+03, atom= 2915 Step= 30, Dmax= 3.6e-03 nm, Epot= -2.93317e+04 Fmax= 1.50419e+03, atom= 2915 Step= 32, Dmax= 2.2e-03 nm, Epot= -2.94725e+04 Fmax= 1.22816e+03, atom= 2655 Step= 33, Dmax= 2.6e-03 nm, Epot= -2.95189e+04 Fmax= 2.07929e+03, atom= 265 Step= 34, Dmax= 3.1e-03 nm, Epot= -2.96589e+04 Fmax= 1.85182e+03, atom= 265 Step= 36, Dmax= 1.9e-03 nm, Epot= -2.98548e+04 Fmax= 5.34297e+02, atom= 265 Step= 37, Dmax= 2.2e-03 nm, Epot= -2.99390e+04 Fmax= 2.26194e+03, atom= 265 Step= 38, Dmax= 2.7e-03 nm, Epot= -3.01610e+04 Fmax= 1.15806e+03, atom= 265 Step= 40, Dmax= 1.6e-03 nm, Epot= -3.02663e+04 Fmax= 8.89263e+02, atom= 265 Step= 41, Dmax= 1.9e-03 nm, Epot= -3.03267e+04 Fmax= 1.56439e+03, atom= 265 Step= 42, Dmax= 2.3e-03 nm, Epot= -3.04302e+04 Fmax= 1.38819e+03, atom= 265 Step= 43, Dmax= 2.8e-03 nm, Epot= -3.04326e+04 Fmax= 2.14342e+03, atom= 265 Step= 44, Dmax= 3.3e-03 nm, Epot= -3.05229e+04 Fmax= 2.11172e+03, atom= 265 Step= 46, Dmax= 2.0e-03 nm, Epot= -3.07386e+04 Fmax= 4.44444e+02, atom= 3015 Step= 47, Dmax= 2.4e-03 nm, Epot= -3.07475e+04 Fmax= 2.60761e+03, atom= 1115 Step= 48, Dmax= 2.9e-03 nm, Epot= -3.10229e+04 Fmax= 1.06520e+03, atom= 1115 Step= 50, Dmax= 1.7e-03 nm, Epot= -3.10917e+04 Fmax= 1.14633e+03, atom= 1115 Step= 53, Dmax= 5.2e-04 nm, Epot= -3.11543e+04 Fmax= 4.89113e+02, atom= 1115 Step= 57, Dmax= 7.8e-05 nm, Epot= -3.11648e+04 Fmax= 3.92112e+02, atom= 1115 Step= 60, Dmax= 2.3e-05 nm, Epot= -3.11683e+04 Fmax= 3.63293e+02, atom= 2465 Step= 65, Dmax= 1.8e-06 nm, Epot= -3.11686e+04 Fmax= 3.61068e+02, atom= 2465 Step= 67, Dmax= 1.1e-06 nm, Epot= -3.07798e+04 Fmax= 3.59693e+02, atom= 1115 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 68 steps, but did not reach the requested Fmax < 1. Potential Energy = -3.1168609e+04 Maximum force = 3.6106821e+02 on atom 2465 Norm of force = 1.3409255e+02 GROMACS reminds you: "It is an unfortunate fact that when you raise the question of the reliability of many simulations you are often told about how much manpower went into it, how large & fast the computer is, how important the problem is, and such things, which are completely irrelevant to the question that was asked." (Richard Hamming)
In [15]:
#Максимальная сила в целом уменьшалась, но со скачками увеличения (связано с особенностями работы алгоритма).
#Начальное значение максимальной силы Fmax= 4.37969e+05
#Конечное значение максимальной силы берём из 65 шага, так как потенциальная энергия в 67 шаге больше -> Fmax= 3.61068e+02
In [16]:
#Добавим в ячейку молекулы воды типа spc.
In [17]:
!gmx solvate -cp b_em -p b -cs spc216 -o b_s
:-) GROMACS - gmx solvate, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx solvate -cp b_em -p b -cs spc216 -o b_s
Reading solute configuration
Reading solvent configuration
Initialising inter-atomic distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary. Note, that this functionality may
be removed in a future GROMACS version. Please, consider
using another file format for your input.
NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------
Generating solvent configuration
Will generate new solvent configuration of 4x3x4 boxes
Solvent box contains 18966 atoms in 6322 residues
Removed 3306 solvent atoms due to solvent-solvent overlap
Removed 5820 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 3280 residues
Generated solvent containing 9840 atoms in 3280 residues
Writing generated configuration to b_s.gro
Output configuration contains 13040 atoms in 3344 residues
Volume : 160.705 (nm^3)
Density : 1043.34 (g/l)
Number of solvent molecules: 3280
Processing topology
Adding line for 3280 solvent molecules with resname (SOL) to topology file (b.top)
Back Off! I just backed up b.top to ./#b.top.1#
GROMACS reminds you: "Welcome to the Power Age" (2 Unlimited)
In [ ]:
#Проведём "утряску" воды
In [18]:
!gmx grompp -f pr -c b_s -p b -o b_pr -maxwarn 1
:-) GROMACS - gmx grompp, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr7 Command line: gmx grompp -f pr -c b_s -p b -o b_pr -maxwarn 1 Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Ignoring obsolete mdp entry 'ns_type' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' NOTE 1 [file pr.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Setting the LD random seed to 2146795242 Generated 1369 of the 2211 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'DPPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Velocities were taken from a Maxwell distribution at 300 K Analysing residue names: There are: 64 Other residues There are: 3280 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group DPPC is 6463.26 Number of degrees of freedom in T-Coupling group SOL is 19677.74 The largest distance between excluded atoms is 0.392 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x40x52, spacing 0.112 0.111 0.111 Estimate for the relative computational load of the PME mesh part: 0.22 This run will generate roughly 2 Mb of data NOTE 2 [file pr.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 10. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 10. There were 2 notes GROMACS reminds you: "Never attribute to malice that which can be adequately explained by stupidity." (Robert Hanlon)
In [19]:
!gmx mdrun -deffnm b_pr -v
:-) GROMACS - gmx mdrun, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr7 Command line: gmx mdrun -deffnm b_pr -v Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see log). Reading file b_pr.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI thread Using 8 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'bilayer in water' 1000 steps, 0.2 ps. step 400, remaining wall clock time: 2 s Step 466, time 0.0932 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006090, max 0.196084 (between atoms 2505 and 2504) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 467, time 0.0934 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.005810, max 0.194382 (between atoms 2505 and 2504) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 468, time 0.0936 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.004209, max 0.132556 (between atoms 2505 and 2504) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 473, time 0.0946 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.014344, max 0.499414 (between atoms 2504 and 2501) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 474, time 0.0948 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.021525, max 0.855704 (between atoms 2504 and 2502) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2504 2502 47.4 0.0776 0.0212 0.1470 2504 2501 57.6 0.0736 0.0300 0.1470 Wrote pdb files with previous and current coordinates Step 475, time 0.095 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007256, max 0.270981 (between atoms 2504 and 2502) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2504 2503 37.0 0.1710 0.1174 0.1470 2504 2502 44.9 0.0212 0.1072 0.1470 2505 2504 36.8 0.1717 0.1318 0.1470 Step 477, time 0.0954 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.044897, max 1.255774 (between atoms 2505 and 2504) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2506 2505 32.5 0.1541 0.0963 0.1530 Wrote pdb files with previous and current coordinates Step 478, time 0.0956 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.872120, max 24.416075 (between atoms 2504 and 2502) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2504 2503 108.9 0.3297 3.7149 0.1470 2504 2502 171.9 0.3256 3.7362 0.1470 2504 2501 104.5 0.3315 3.7248 0.1470 2505 2504 100.1 0.3316 3.7195 0.1470 2506 2505 92.3 0.0963 0.7832 0.1530 Wrote pdb files with previous and current coordinates Step 479, time 0.0958 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.432773, max 13.273639 (between atoms 2505 and 2504) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2504 2503 98.4 3.7149 1.7262 0.1470 2504 2502 93.5 3.7362 1.7999 0.1470 2504 2501 97.3 3.7248 1.9555 0.1470 2505 2504 97.2 3.7195 2.0982 0.1470 2506 2505 51.4 0.7832 0.2102 0.1530 2509 2508 30.1 0.1495 0.1607 0.1480 2510 2508 31.5 0.1478 0.1627 0.1480 2507 2506 88.2 0.1665 0.7463 0.1430 Wrote pdb files with previous and current coordinates Step 480, time 0.096 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.758434, max 50.126419 (between atoms 2504 and 2502) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2504 2503 126.1 1.7262 7.4377 0.1470 2504 2502 131.5 1.7999 7.5156 0.1470 2504 2501 125.9 1.9555 7.4111 0.1470 2505 2504 144.3 2.0982 6.7230 0.1470 2506 2505 96.4 0.2102 2.6830 0.1530 2508 2507 90.0 0.1737 0.3830 0.1610 2509 2508 33.6 0.1607 0.1628 0.1480 2511 2508 31.9 0.1732 0.1766 0.1610 2507 2506 84.9 0.7463 0.4883 0.1430 2512 2511 34.1 0.1469 0.1563 0.1430 step 480: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates
In [20]:
#Step 480, time 0.096 (ps) LINCS WARNING
#relative constraint deviation after LINCS:
#rms 1.758434, max 50.126419 (between atoms 2504 and 2502)
#bonds that rotated more than 30 degrees:
# atom 1 atom 2 angle previous, current, constraint length
# 2504 2503 126.1 1.7262 7.4377 0.1470
# 2504 2502 131.5 1.7999 7.5156 0.1470
# 2504 2501 125.9 1.9555 7.4111 0.1470
# 2505 2504 144.3 2.0982 6.7230 0.1470
# 2506 2505 96.4 0.2102 2.6830 0.1530
# 2508 2507 90.0 0.1737 0.3830 0.1610
# 2509 2508 33.6 0.1607 0.1628 0.1480
# 2511 2508 31.9 0.1732 0.1766 0.1610
# 2507 2506 84.9 0.7463 0.4883 0.1430
# 2512 2511 34.1 0.1469 0.1563 0.1430
#step 480: One or more water molecules can not be settled.
#Check for bad contacts and/or reduce the timestep if appropriate.
#Wrote pdb files with previous and current coordinates
#Произошёл взрыв системы, сделаем MD немного иначе
In [21]:
!gmx grompp -f em -c b_s -p b -o b_empr -maxwarn 1
!gmx mdrun -deffnm b_empr -v
:-) GROMACS - gmx grompp, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx grompp -f em -c b_s -p b -o b_empr -maxwarn 1
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -1381010450
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
WARNING 1 [file b.top, line 21]:
The following macros were defined in the 'define' mdp field with the -D
prefix, but were not used in the topology:
FLEX_SPC
If you haven't made a spelling error, either use the macro you defined,
or don't define the macro
Analysing residue names:
There are: 64 Other residues
There are: 3280 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 29277.00
NOTE 2 [file em.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 305 Mb of data
There were 2 notes
There was 1 warning
GROMACS reminds you: "Men love to wonder, and that is the seed of science." (Ralph Waldo Emerson)
:-) GROMACS - gmx mdrun, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx mdrun -deffnm b_empr -v
Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see
log).
Reading file b_empr.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled.
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 1000000
Step= 0, Dmax= 2.0e-02 nm, Epot= 7.92112e+05 Fmax= 3.53767e+05, atom= 1105
Step= 1, Dmax= 2.0e-02 nm, Epot= 4.71422e+05 Fmax= 1.67776e+05, atom= 1100
Step= 2, Dmax= 2.4e-02 nm, Epot= 3.00471e+05 Fmax= 1.07214e+05, atom= 6777
Step= 3, Dmax= 2.9e-02 nm, Epot= 2.02391e+05 Fmax= 6.93209e+04, atom= 6777
Step= 4, Dmax= 3.5e-02 nm, Epot= 1.35266e+05 Fmax= 8.26849e+04, atom= 6777
Step= 5, Dmax= 4.1e-02 nm, Epot= 1.05056e+05 Fmax= 1.87282e+04, atom= 6777
Step= 6, Dmax= 5.0e-02 nm, Epot= 3.70596e+04 Fmax= 7.49586e+04, atom= 6777
step 7: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step= 8, Dmax= 3.0e-02 nm, Epot= 3.09795e+04 Fmax= 1.31742e+04, atom= 1099
Step= 9, Dmax= 3.6e-02 nm, Epot= 1.15810e+04 Fmax= 1.41548e+04, atom= 1075
Step= 10, Dmax= 4.3e-02 nm, Epot= -1.31752e+03 Fmax= 2.33228e+04, atom= 1075
Step= 11, Dmax= 5.2e-02 nm, Epot= -7.83959e+03 Fmax= 2.13372e+04, atom= 1075
Step= 13, Dmax= 3.1e-02 nm, Epot= -1.46188e+04 Fmax= 1.45767e+04, atom= 2415
Step= 14, Dmax= 3.7e-02 nm, Epot= -1.51973e+04 Fmax= 3.18636e+04, atom= 2865
Step= 15, Dmax= 4.5e-02 nm, Epot= -2.10550e+04 Fmax= 2.39658e+04, atom= 2865
Step= 17, Dmax= 2.7e-02 nm, Epot= -2.86867e+04 Fmax= 1.01313e+04, atom= 2415
Step= 19, Dmax= 1.6e-02 nm, Epot= -3.12890e+04 Fmax= 1.06232e+04, atom= 1565
Step= 20, Dmax= 1.9e-02 nm, Epot= -3.50332e+04 Fmax= 1.46097e+04, atom= 1565
Step= 21, Dmax= 2.3e-02 nm, Epot= -3.77615e+04 Fmax= 1.54190e+04, atom= 1565
Step= 22, Dmax= 2.8e-02 nm, Epot= -4.07412e+04 Fmax= 2.08262e+04, atom= 1565
Step= 23, Dmax= 3.3e-02 nm, Epot= -4.27297e+04 Fmax= 2.15664e+04, atom= 1565
Step= 24, Dmax= 4.0e-02 nm, Epot= -4.41666e+04 Fmax= 3.06763e+04, atom= 1565
Step= 25, Dmax= 4.8e-02 nm, Epot= -4.47437e+04 Fmax= 3.03374e+04, atom= 1565
Step= 27, Dmax= 2.9e-02 nm, Epot= -5.13734e+04 Fmax= 5.21136e+03, atom= 1565
Step= 29, Dmax= 1.7e-02 nm, Epot= -5.33573e+04 Fmax= 1.77918e+04, atom= 1565
Step= 30, Dmax= 2.1e-02 nm, Epot= -5.73311e+04 Fmax= 9.04743e+03, atom= 1565
Step= 31, Dmax= 2.5e-02 nm, Epot= -5.78268e+04 Fmax= 2.23311e+04, atom= 1565
Step= 32, Dmax= 3.0e-02 nm, Epot= -6.23330e+04 Fmax= 1.54797e+04, atom= 1565
Step= 34, Dmax= 1.8e-02 nm, Epot= -6.38990e+04 Fmax= 7.86523e+03, atom= 1565
Step= 35, Dmax= 2.1e-02 nm, Epot= -6.55819e+04 Fmax= 1.93276e+04, atom= 1565
Step= 36, Dmax= 2.6e-02 nm, Epot= -6.76766e+04 Fmax= 1.40517e+04, atom= 1565
Step= 37, Dmax= 3.1e-02 nm, Epot= -6.79855e+04 Fmax= 2.65268e+04, atom= 1565
Step= 38, Dmax= 3.7e-02 nm, Epot= -7.02412e+04 Fmax= 2.12711e+04, atom= 1565
Step= 40, Dmax= 2.2e-02 nm, Epot= -7.40097e+04 Fmax= 6.89162e+03, atom= 1565
Step= 42, Dmax= 1.3e-02 nm, Epot= -7.47277e+04 Fmax= 1.06012e+04, atom= 1565
Step= 43, Dmax= 1.6e-02 nm, Epot= -7.65337e+04 Fmax= 1.00359e+04, atom= 1565
Step= 44, Dmax= 1.9e-02 nm, Epot= -7.75452e+04 Fmax= 1.48827e+04, atom= 1565
Step= 45, Dmax= 2.3e-02 nm, Epot= -7.94689e+04 Fmax= 1.51902e+04, atom= 1565
Step= 47, Dmax= 1.4e-02 nm, Epot= -8.10504e+04 Fmax= 3.16031e+03, atom= 1565
Step= 48, Dmax= 1.7e-02 nm, Epot= -8.31318e+04 Fmax= 1.75026e+04, atom= 1565
Step= 49, Dmax= 2.0e-02 nm, Epot= -8.51421e+04 Fmax= 8.41832e+03, atom= 1565
Step= 50, Dmax= 2.4e-02 nm, Epot= -8.54398e+04 Fmax= 2.23487e+04, atom= 1565
Step= 51, Dmax= 2.9e-02 nm, Epot= -8.78983e+04 Fmax= 1.47383e+04, atom= 1565
Step= 53, Dmax= 1.7e-02 nm, Epot= -8.93305e+04 Fmax= 7.39845e+03, atom= 1565
Step= 55, Dmax= 1.0e-02 nm, Epot= -9.00289e+04 Fmax= 6.05438e+03, atom= 1565
Step= 56, Dmax= 1.2e-02 nm, Epot= -9.16562e+04 Fmax= 1.00916e+04, atom= 1565
Step= 57, Dmax= 1.5e-02 nm, Epot= -9.18610e+04 Fmax= 9.29900e+03, atom= 1565
Step= 58, Dmax= 1.8e-02 nm, Epot= -9.25663e+04 Fmax= 1.39224e+04, atom= 1565
Step= 59, Dmax= 2.1e-02 nm, Epot= -9.38971e+04 Fmax= 1.38387e+04, atom= 1415
Step= 60, Dmax= 2.6e-02 nm, Epot= -9.43564e+04 Fmax= 1.96429e+04, atom= 1415
Step= 61, Dmax= 3.1e-02 nm, Epot= -9.49379e+04 Fmax= 1.95885e+04, atom= 1565
Step= 63, Dmax= 1.9e-02 nm, Epot= -9.79755e+04 Fmax= 3.68631e+03, atom= 1565
Step= 65, Dmax= 1.1e-02 nm, Epot= -9.85334e+04 Fmax= 1.10611e+04, atom= 1015
Step= 66, Dmax= 1.3e-02 nm, Epot= -1.00415e+05 Fmax= 6.54777e+03, atom= 1015
Step= 68, Dmax= 8.0e-03 nm, Epot= -1.01442e+05 Fmax= 4.00616e+03, atom= 1015
Step= 69, Dmax= 9.6e-03 nm, Epot= -1.02168e+05 Fmax= 7.93736e+03, atom= 1015
Step= 70, Dmax= 1.2e-02 nm, Epot= -1.03331e+05 Fmax= 7.17332e+03, atom= 1015
Step= 71, Dmax= 1.4e-02 nm, Epot= -1.03822e+05 Fmax= 1.10522e+04, atom= 1015
Step= 72, Dmax= 1.7e-02 nm, Epot= -1.04562e+05 Fmax= 1.06820e+04, atom= 1015
Step= 74, Dmax= 1.0e-02 nm, Epot= -1.06587e+05 Fmax= 2.59835e+03, atom= 1015
Step= 76, Dmax= 6.0e-03 nm, Epot= -1.07030e+05 Fmax= 5.70026e+03, atom= 1015
Step= 77, Dmax= 7.2e-03 nm, Epot= -1.08323e+05 Fmax= 3.41699e+03, atom= 1015
Step= 79, Dmax= 4.3e-03 nm, Epot= -1.08825e+05 Fmax= 2.63465e+03, atom= 2058
Step= 80, Dmax= 5.2e-03 nm, Epot= -1.09799e+05 Fmax= 4.28581e+03, atom= 2058
Step= 81, Dmax= 6.2e-03 nm, Epot= -1.10610e+05 Fmax= 3.56098e+03, atom= 8
Step= 82, Dmax= 7.4e-03 nm, Epot= -1.10787e+05 Fmax= 6.14212e+03, atom= 1015
Step= 83, Dmax= 8.9e-03 nm, Epot= -1.11772e+05 Fmax= 5.70116e+03, atom= 1015
Step= 84, Dmax= 1.1e-02 nm, Epot= -1.11899e+05 Fmax= 8.25327e+03, atom= 1015
Step= 85, Dmax= 1.3e-02 nm, Epot= -1.12814e+05 Fmax= 8.64717e+03, atom= 1015
Step= 87, Dmax= 7.7e-03 nm, Epot= -1.13807e+05 Fmax= 1.61364e+03, atom= 2815
Step= 89, Dmax= 4.6e-03 nm, Epot= -1.14523e+05 Fmax= 4.83960e+03, atom= 1015
Step= 90, Dmax= 5.5e-03 nm, Epot= -1.15313e+05 Fmax= 2.87196e+03, atom= 758
Step= 91, Dmax= 6.7e-03 nm, Epot= -1.16000e+05 Fmax= 5.81735e+03, atom= 758
Step= 92, Dmax= 8.0e-03 nm, Epot= -1.17228e+05 Fmax= 4.33334e+03, atom= 1015
Step= 93, Dmax= 9.6e-03 nm, Epot= -1.17285e+05 Fmax= 8.54556e+03, atom= 1015
Step= 94, Dmax= 1.1e-02 nm, Epot= -1.18191e+05 Fmax= 6.49945e+03, atom= 1015
Step= 96, Dmax= 6.9e-03 nm, Epot= -1.19007e+05 Fmax= 2.66604e+03, atom= 1015
Step= 97, Dmax= 8.3e-03 nm, Epot= -1.19194e+05 Fmax= 8.30075e+03, atom= 1015
Step= 98, Dmax= 9.9e-03 nm, Epot= -1.20305e+05 Fmax= 4.75641e+03, atom= 1015
Step= 99, Dmax= 1.2e-02 nm, Epot= -1.20411e+05 Fmax= 1.06268e+04, atom= 1015
Step= 100, Dmax= 1.4e-02 nm, Epot= -1.21646e+05 Fmax= 8.10604e+03, atom= 1015
Step= 102, Dmax= 8.6e-03 nm, Epot= -1.22645e+05 Fmax= 2.92036e+03, atom= 2215
Step= 104, Dmax= 5.2e-03 nm, Epot= -1.23588e+05 Fmax= 4.18195e+03, atom= 2215
Step= 105, Dmax= 6.2e-03 nm, Epot= -1.23619e+05 Fmax= 4.04825e+03, atom= 2215
Step= 106, Dmax= 7.4e-03 nm, Epot= -1.24135e+05 Fmax= 5.95396e+03, atom= 2215
Step= 107, Dmax= 8.9e-03 nm, Epot= -1.24784e+05 Fmax= 5.76171e+03, atom= 2215
Step= 108, Dmax= 1.1e-02 nm, Epot= -1.24995e+05 Fmax= 8.67534e+03, atom= 2215
Step= 109, Dmax= 1.3e-02 nm, Epot= -1.25565e+05 Fmax= 8.05975e+03, atom= 2215
Step= 111, Dmax= 7.7e-03 nm, Epot= -1.26736e+05 Fmax= 2.33628e+03, atom= 3655
Step= 113, Dmax= 4.6e-03 nm, Epot= -1.27220e+05 Fmax= 3.57215e+03, atom= 365
Step= 114, Dmax= 5.5e-03 nm, Epot= -1.27835e+05 Fmax= 4.05785e+03, atom= 1765
Step= 115, Dmax= 6.6e-03 nm, Epot= -1.28286e+05 Fmax= 5.01561e+03, atom= 365
Step= 116, Dmax= 8.0e-03 nm, Epot= -1.28878e+05 Fmax= 5.65579e+03, atom= 365
Step= 117, Dmax= 9.6e-03 nm, Epot= -1.29230e+05 Fmax= 7.15830e+03, atom= 365
Step= 118, Dmax= 1.1e-02 nm, Epot= -1.29544e+05 Fmax= 8.24423e+03, atom= 365
Step= 119, Dmax= 1.4e-02 nm, Epot= -1.30150e+05 Fmax= 9.99008e+03, atom= 365
Step= 121, Dmax= 8.3e-03 nm, Epot= -1.31496e+05 Fmax= 1.36653e+03, atom= 1158
Step= 124, Dmax= 2.5e-03 nm, Epot= -1.31916e+05 Fmax= 2.42168e+03, atom= 2808
Step= 125, Dmax= 3.0e-03 nm, Epot= -1.32435e+05 Fmax= 1.85067e+03, atom= 1658
Step= 126, Dmax= 3.6e-03 nm, Epot= -1.32587e+05 Fmax= 3.99400e+03, atom= 308
Step= 127, Dmax= 4.3e-03 nm, Epot= -1.33321e+05 Fmax= 2.12447e+03, atom= 308
Step= 128, Dmax= 5.1e-03 nm, Epot= -1.33458e+05 Fmax= 5.30095e+03, atom= 308
Step= 129, Dmax= 6.2e-03 nm, Epot= -1.34098e+05 Fmax= 2.68546e+03, atom= 308
Step= 131, Dmax= 3.7e-03 nm, Epot= -1.34583e+05 Fmax= 2.39261e+03, atom= 3088
Step= 133, Dmax= 2.2e-03 nm, Epot= -1.34814e+05 Fmax= 1.47389e+03, atom= 2058
Step= 134, Dmax= 2.7e-03 nm, Epot= -1.35221e+05 Fmax= 2.94349e+03, atom= 2808
Step= 135, Dmax= 3.2e-03 nm, Epot= -1.35479e+05 Fmax= 2.08539e+03, atom= 1658
Step= 136, Dmax= 3.8e-03 nm, Epot= -1.35840e+05 Fmax= 3.62378e+03, atom= 1658
Step= 137, Dmax= 4.6e-03 nm, Epot= -1.36064e+05 Fmax= 2.89435e+03, atom= 1658
Step= 138, Dmax= 5.5e-03 nm, Epot= -1.36284e+05 Fmax= 4.61941e+03, atom= 308
Step= 139, Dmax= 6.6e-03 nm, Epot= -1.36303e+05 Fmax= 4.10654e+03, atom= 1658
Step= 140, Dmax= 8.0e-03 nm, Epot= -1.36913e+05 Fmax= 6.01385e+03, atom= 1658
Step= 141, Dmax= 9.6e-03 nm, Epot= -1.36916e+05 Fmax= 6.01823e+03, atom= 1658
Step= 142, Dmax= 1.1e-02 nm, Epot= -1.37200e+05 Fmax= 9.34582e+03, atom= 3015
Step= 143, Dmax= 1.4e-02 nm, Epot= -1.37684e+05 Fmax= 8.98007e+03, atom= 3015
Step= 144, Dmax= 1.7e-02 nm, Epot= -1.37869e+05 Fmax= 1.33326e+04, atom= 3015
Step= 145, Dmax= 2.0e-02 nm, Epot= -1.37914e+05 Fmax= 1.26994e+04, atom= 3015
Step= 147, Dmax= 1.2e-02 nm, Epot= -1.40258e+05 Fmax= 2.93566e+03, atom= 3015
Step= 150, Dmax= 3.6e-03 nm, Epot= -1.40281e+05 Fmax= 2.35624e+03, atom= 3015
Step= 151, Dmax= 4.3e-03 nm, Epot= -1.40463e+05 Fmax= 3.17064e+03, atom= 3015
Step= 152, Dmax= 5.1e-03 nm, Epot= -1.40850e+05 Fmax= 4.19970e+03, atom= 3015
Step= 153, Dmax= 6.2e-03 nm, Epot= -1.41364e+05 Fmax= 3.84805e+03, atom= 3015
Step= 155, Dmax= 3.7e-03 nm, Epot= -1.41661e+05 Fmax= 1.85970e+03, atom= 1658
Step= 156, Dmax= 4.4e-03 nm, Epot= -1.41867e+05 Fmax= 3.92424e+03, atom= 8
Step= 157, Dmax= 5.3e-03 nm, Epot= -1.42316e+05 Fmax= 3.49137e+03, atom= 8
Step= 158, Dmax= 6.4e-03 nm, Epot= -1.42756e+05 Fmax= 5.21012e+03, atom= 8
Step= 160, Dmax= 3.8e-03 nm, Epot= -1.43460e+05 Fmax= 1.15396e+03, atom= 2808
Step= 164, Dmax= 5.7e-04 nm, Epot= -1.43467e+05 Fmax= 1.75472e+03, atom= 2088
Step= 166, Dmax= 3.4e-04 nm, Epot= -1.43556e+05 Fmax= 1.12428e+03, atom= 26588
Step= 169, Dmax= 1.0e-04 nm, Epot= -1.43597e+05 Fmax= 9.66970e+02, atom= 99217
Step= 172, Dmax= 3.1e-05 nm, Epot= -1.43612e+05 Fmax= 1.00257e+03, atom= 758
Step= 176, Dmax= 4.7e-06 nm, Epot= -1.43614e+05 Fmax= 9.63996e+02, atom= 9921
Step= 178, Dmax= 2.8e-06 nm, Epot= -1.43615e+05 Fmax= 9.63748e+02, atom= 9921
Step= 180, Dmax= 1.7e-06 nm, Epot= -1.43414e+05 Fmax= 9.98840e+02, atom= 758
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 181 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -1.4361534e+05
Maximum force = 9.6374780e+02 on atom 9921
Norm of force = 1.9308007e+02
GROMACS reminds you: "The way to succeed is to double your failure rate." (Thomas J. Watson)
In [22]:
!gmx grompp -f pr -c b_empr -p b -o b_pr -maxwarn 1
!gmx mdrun -deffnm b_pr -v
:-) GROMACS - gmx grompp, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx grompp -f pr -c b_empr -p b -o b_pr -maxwarn 1
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
NOTE 1 [file pr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider
setting nstcomm equal to nstcalcenergy for less overhead
Setting the LD random seed to -413796449
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'DPPC'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Velocities were taken from a Maxwell distribution at 300 K
Analysing residue names:
There are: 64 Other residues
There are: 3280 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group DPPC is 6463.26
Number of degrees of freedom in T-Coupling group SOL is 19677.74
The largest distance between excluded atoms is 0.409 nm
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x40x52, spacing 0.112 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 2 Mb of data
NOTE 2 [file pr.mdp]:
COM removal frequency is set to (1).
Other settings require a global communication frequency of 10.
Note that this will require additional global communication steps,
which will reduce performance when using multiple ranks.
Consider setting nstcomm to a multiple of 10.
There were 2 notes
Back Off! I just backed up b_pr.tpr to ./#b_pr.tpr.1#
GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann)
:-) GROMACS - gmx mdrun, 2022.5-Debian_2022.5_2 (-:
Executable: /bin/gmx
Data prefix: /usr
Working dir: /home/students/y22/urazov.d/term8/Pr7
Command line:
gmx mdrun -deffnm b_pr -v
Back Off! I just backed up b_pr.log to ./#b_pr.log.1#
Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see
log).
Reading file b_pr.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1
Using 1 MPI thread
Using 8 OpenMP threads
NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled.
Back Off! I just backed up b_pr.xtc to ./#b_pr.xtc.1#
Back Off! I just backed up b_pr.trr to ./#b_pr.trr.1#
Back Off! I just backed up b_pr.edr to ./#b_pr.edr.1#
starting mdrun 'bilayer in water'
1000 steps, 0.2 ps.
step 900, remaining wall clock time: 0 s
Writing final coordinates.
step 1000, remaining wall clock time: 0 s
Core t (s) Wall t (s) (%)
Time: 26.282 3.285 800.0
(ns/day) (hour/ns)
Performance: 5.265 4.559
GROMACS reminds you: "Nobody ever complained a seminar was too easy to understand." (Ken Dill)
In [23]:
#Переформатируем b_pr.gro и b_s.gro в pdb формат.
#Сравним визуально в PyMol изменения в системах.
!gmx editconf -f b_pr.gro -o b_pr.pdb
:-) GROMACS - gmx editconf, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr7 Command line: gmx editconf -f b_pr.gro -o b_pr.pdb Note that major changes are planned in future for editconf, to improve usability and utility. Read 13040 atoms Volume: 160.705 nm^3, corresponds to roughly 72300 electrons Velocities found GROMACS reminds you: "Not to get technical... but according to chemistry, alcohol is a solution." (Anonymous)
In [24]:
!gmx editconf -f b_s.gro -o b_s.pdb
:-) GROMACS - gmx editconf, 2022.5-Debian_2022.5_2 (-: Executable: /bin/gmx Data prefix: /usr Working dir: /home/students/y22/urazov.d/term8/Pr7 Command line: gmx editconf -f b_s.gro -o b_s.pdb Note that major changes are planned in future for editconf, to improve usability and utility. Read 13040 atoms Volume: 160.705 nm^3, corresponds to roughly 72300 electrons No velocities found GROMACS reminds you: "The Nobel Prize is fine, but the drugs I've developed are rewards in themselves." (Gertrude Elion)
In [25]:
Image(filename='b_s.png')
Out[25]:
In [26]:
Image(filename='b_pr.png')
Out[26]:
In [27]:
# Можно заметить изменение в топологии: липиды больше не расположены идеально ровно
In [30]:
#Подготовим файлы к загрузке на суперкомпьютер
!cd ..
!scp -r ./Pr7 lom:_scratch/fbb
ssh: Could not resolve hostname lom: Name or service not known scp: Connection closed
In [2]:
# Макарыч: fbbmm
# ag8fbqRQgl
# Не получилось зайти (хмм)
In [ ]: