• Force field -- coarse-grain
• System charge -- 4.000000 (due to lysines), but optimization process says "removing all charge groups because cutoff-scheme=Verlet" (seems like some algorithm trick, not real physical removing)
• Shape of the cell --1x1x1 box
• Volume of the box -- 343 nm$^3$
• Minimization energy algorithm -- steepest descent
• Calculating electrostatics algorithm -- Reaction-Field
• Calculating VdW algorithm -- Cut-off
• Solvent model -- W3=SPC/TIP3p, W4=TIP4p (single or pairs)
• Another information about solvent and everything that connects to it -- no information due to molecular dynamics type!
• Algorithm time -- 2672.437 sec
• Number of processors -- "running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs", but "using 1 MPI thread and 1 OpenMP thread"
• Number of steps -- 1000000 (default in mdp file), but we force it to 3000000
• Time step -- 0.01 (ps)
• Integrator -- md (a leap-frog algorithm for integrating Newton's equations of motion)
• Thermostate algorithm -- V-rescale
• Barostate algorithm -- Parrinello-Rahman

import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np

x=np.genfromtxt("files/COLVAR")
plt.plot(x[:, 0],x[:, 1])
sns.despine()
plt.xlabel("Time, ps")
plt.ylabel("Distance, nm")

Text(0, 0.5, 'Distance, nm')

import subprocess

def com_exec(command):
    rt = subprocess.run(command, shell=True, stderr=subprocess.PIPE)
    return print(rt.stderr.decode('utf-8'))

com_exec("echo 0 13 | gmx trjconv -f files/meta.trr -s files/meta.tpr -conect -o files/meta.pdb -pbc mol")

import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]

import pymol
import IPython
pymol.finish_launching()
from pymol import cmd,stored

cmd.load("files/meta.pdb")
cmd.bg_color("white")

cmd.hide("all")
cmd.show("nb_spheres", "resn w")
cmd.show("sticks", "resn dppc or resi 1-23")
cmd.color("pink", "resi 1-23")
cmd.color("silver", "resn dppc")
cmd.color("blue", "resn w")

import os
import IPython
cmd.set('ray_trace_mode', 0)
cmd.png(os.path.join("files",'n_frame.png'), '1200', '720', ray=1)

IPython.display.Image(os.path.join("files",'n_frame.png'), retina=True)