jandronis / md-gromacs-tip4p2005

An example of running water MD simulations with gromacs using TIP4P/2005

MD-Gromacs_TIP4P-2005

An example of running water MD simulations with gromacs using TIP4P/2005

Simulating a water box based on this tutorial https://group.miletic.net/en/tutorials/gromacs/1-tip4pew-water/

Here I modified CHARMM36 to add TIP4P/2005 http://mackerell.umaryland.edu/charmm_ff.shtml

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Create topology

Make topology file (topol.top) including the following

#include "./charmm36-jul2021.ff/forcefield.itp"
#include "./charmm36-jul2021.ff/tip4p2005.itp"

[ System ]
TIP4P2005

[ Molecules]

Prepare and run MD

Add water molecules

gmx solvate -cs tip4p -o box.gro -box 3 3 3 -p topol.top

Energy minimization

gmx grompp -f mdp/em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

NVT equilibration

gmx grompp -f mdp/nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt

NPT equilibration

gmx grompp -f mdp/npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -deffnm npt

MD run

gmx grompp -f mdp/md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
gmx mdrun -deffnm md_0_1

Analyze results

Make molecules whole

gmx trjconv -s md_0_1.tpr -f md_0_1.trr -o md_0_1_noPBC.trr -pbc mol

Calculate O-O radial distributions

gmx rdf -f md_0_1_noPBC.trr -s md_0_1.tpr -ref 'name OW' -sel 'name OW'

Make index file and calculate velocity autocorrelations

gmx make_ndx -f md_0_1.gro
gmx velacc -f md_0_1_noPBC.trr -s md_0_1.tpr -n index.ndx -os -mol -recip

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Run it on HPC

To run this on HPC see notes.txt. Here I use HPC2N, project number: SNIC2021-22-656.

To connect on the HPC2N use

ssh [email protected]

To activate GROMACS and it's prerequisites use:

ml GCC/10.2.0  CUDA/11.1.1  OpenMPI/4.0.5
ml GCC/10.2.0  OpenMPI/4.0.5
ml GROMACS/2021

Submit jobs by

sbatch slurm/cpu.sh

Check status by

squeue -u username