/gromacs-ion-water-simulation

This repository contained python code used to do ion water system simulation.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

gromacs-ion-water-simulation

This repository contained python code used to do ion water system simulation.

Authors:

Ruan Yang
Email: ruanyang_njut@163.com

Required library:

MDAnalysis； https://github.com/MDAnalysis/mdanalysis

Usage:

Gmxmdp.py: Generated GROMACS .mdp file. Simulation process: EM---NVTEquilibrium---NPTEquilibrium---NVT(NPT) Production run---Standmdp. reference: https://github.com/ruanyangry/gromacs-lammps-process-simulation.

FF.py: Generated GROMACS .top file and ionwater.sh.

gmxndx.py: Generated GROMACS .ndx file.

# _*_ coding:utf-8 _*_

import Gmxmdp as GMP
import FF 
import os

amber03={"IB+":1.000,"CA":2.000,"CL":-1.000,"NA":1.000,"MG":2.000,\
"K":1.000,"RB":1.000,"CS":1.000,"LI":1.000,"ZN":2.000,"water":["spce",\
"spc","tip3p","tip4p","tip4pew","tip5p"]}

charmm27={"NA":1.000,"MG":2.000,"K":1.000,"CS":1.000,"CA":2.000,"CL":-1.000,\
"ZN":2.000,"water":["spc","spce","tip3p","tip4p","tip5p","tips3p"]}

charmm36={"LI":[1.000,"LIT","LI"],"NA":[1.000,"SOD","NA"],"K":[1.000,"POT","K"],\
"CS":[1.000,"CES","Ces"],"CL":[-1.000,"CLA","CL"],"CA":[2.000,"CAL","Cal"],\
"MG":[2.000,"MGA","MG"],"ZN":[2.000,"ZN","ZN"],"water":["spc","spce","tip3p","tip4p"]}

oplsaa={"MG":2.000,"CA":2.000,"LI":1.000,"NA":1.000,"K":1.000,"RB":1.000,\
"CS":1.000,"F":-1.000,"CL":-1.000,"BR":-1.000,"I":-1.000,"water":["spc",\
"spce","tip3p","tip4p","tip4pew","tip5p","tip5pe"]}

gromos54a7={"CU1":1.000,"CU":2.000,"ZN":2.000,"MG":2.000,"CA":2.000,"NA":1.000,\
"CL":-1.000,"water":["spc","spce","tip3p","tip4p"]}

FF.writetop("amber03.ff",amber03["water"][2],["NA",amber03["NA"],1],\
["CL",amber03["CL"],1],16)

GMP.nemd(ensemble='nvt',integrator='md',nsteps=500000,dt=0.002,outfrequency=500,\
constraints='all-bonds',rcoulomb=1.2,rvdw=1.2,tcoupl='V-rescale',ref_t=300.0,pcoupl='Parrinello-Rahman',\
pcoupltype='isotropic',ref_p=1.0,nemd=["electric-field",1.0])

GMP.Equilibrium(ensemble='nvt',integrator='md',nsteps=500000,dt=0.002,outfrequency=500,\
constraints='all-bonds',rcoulomb=1.2,rvdw=1.2,tcoupl='V-rescale',ref_t=300.0,pcoupl='no',\
pcoupltype='isotropic',ref_p=1.0)

GMP.Equilibrium(ensemble='npt',integrator='md',nsteps=2000000,dt=0.002,outfrequency=500,\
constraints='all-bonds',rcoulomb=1.2,rvdw=1.2,tcoupl='V-rescale',ref_t=300.0,pcoupl='Parrinello-Rahman',\
pcoupltype='isotropic',ref_p=1.0)

os.system("dos2unix ionwater.sh")
os.system("qsub ionwater.sh")

Analysis methods in ionwateranalysis-v3.py:

  1. Radial distribution functions for ow-ow、ow-hw、cation-ow and anion-ow.
  2. The coordination numbers for the first and second shells of ions.
  3. Probability distributions of water dipole orientation.-OH and -HH.
  4. Probability distributions of the orientation angle α and θ of water molecules in the first and second hydration shells.
  5. Analyzing hydrogen bond lifetimes (HBL) and hydrogen bond (HB) in ions first or second hydration shells and between first and second hydration shells.
  6. Mean square displacement (MSD) of ions and water along x y z and the total displacment.
  7. Analyzing survival probability (SP) SurvivalProbability for water molecules in ions hydration shells.

The analysis codes can automatically obtain the radius of the ions first and second hydration layer.

python ionwateranalysis-v3.py -gro "nvtnemd.gro" -trr "nvtnemd.trr" -tpr "nvtnemd.tpr" -cationname "NA" -anionname "CL"  

parser=argparse.ArgumentParser(description="Analysis ion water systems.\
Using MDAnalysis library.")
parser.add_argument('-gro',dest='GRO',type=str,help='The name of .gro file')
parser.add_argument('-trr',dest='TRR',type=str,help='The name of .trr file')
parser.add_argument('-tpr',dest='TPR',type=str,help='The name of .tpr file')
parser.add_argument('-cationname',dest='cationname',type=str,help='the name of cation ions')
parser.add_argument('-anionname',dest='anionname',type=str,help='the name of anion ions')

args = parser.parse_args()
GRO=args.GRO
TRR=args.TRR
TPR=args.TPR
cationname=args.cationname
anionname=args.anionname

References: https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html

Citation:

These publications associated with this code is found here:

  1. Molecular Dynamics Study of Mg2+/Li+ Separation via Biomimetic Graphene-Based Nanopores: The Role of Dehydration in Second Shell. DOI: 10.1021/acs.langmuir.6b03001.

  2. Mg2+-Channel-Inspired Nanopores for Mg2+/Li+ Separation: The Effect of Coordination on the Ionic Hydration Microstructure. DOI: 10.1021/acs.langmuir.7b01249.