This repository contained python code used to do ion water system simulation.
Ruan Yang
Email: [email protected]
Required library:
MDAnalysis； https://github.com/MDAnalysis/mdanalysis
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")
- Radial distribution functions for ow-ow、ow-hw、cation-ow and anion-ow.
- The coordination numbers for the first and second shells of ions.
- Probability distributions of water dipole orientation.-OH and -HH.
- Probability distributions of the orientation angle α and θ of water molecules in the first and second hydration shells.
- Analyzing hydrogen bond lifetimes (HBL) and hydrogen bond (HB) in ions first or second hydration shells and between first and second hydration shells.
- Mean square displacement (MSD) of ions and water along x y z and the total displacment.
- 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
These publications associated with this code is found here:
-
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.
-
Mg2+-Channel-Inspired Nanopores for Mg2+/Li+ Separation: The Effect of Coordination on the Ionic Hydration Microstructure. DOI: 10.1021/acs.langmuir.7b01249.