[gmx-users] auto-neutralize system

Samuel Flores samuelfloresc at gmail.com
Fri Feb 19 11:38:03 CET 2016


Is there a way  you know a way to avoid using e.g. -np to explicitly specify number of ions? I would prefer to let GROMACS figure out how many ions it needs to neutralize the system. Mostly this is because I am writing a script to generate SLURM job files for a bunch of variants, and adding up the charges means more coding for me. My system is Staphylococcal Protein A , domain B, in solvent.

I append below the sort of job file I would be having my script generate.

Many thanks


#!/bin/bash -l
#SBATCH -p node
#SBATCH -n 16
#SBATCH --exclusive
#SBATCH -A snic2015-1-443
#SBATCH -t 72:00:00

module add gromacs/5.1.1
cd /home/samuelf/projects/SpA-ZEMu-method-upgrade/C-130-F
# was /proj/snic2015-1-317/GROMACS/GROMACS/BF-SPA/C-130-F/
echo 6 > temp.txt
echo 1 >> temp.txt

cat temp.txt | gmx_mpi pdb2gmx -f last.2.pdb -o last.2_processed.gro -ignh
#6: Amber sb99 , 3 point TIP3P water model: force field was selected based on this benchmark article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/ <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/>
gmx_mpi editconf -f last.2_processed.gro -o last.2_newbox.gro -c -d 1.0 -bt cubic
gmx_mpi solvate -cp last.2_newbox.gro -cs spc216.gro -o last.2_solv.gro -p topol.top

gmx_mpi grompp -f ions.mdp -c last.2_solv.gro -p topol.top -o ions.tpr
echo 13 | gmx_mpi genion -s ions.tpr -o last.2_solv_ions.gro -p topol.top -pname NA -np 5
mpirun -np 16 gmx_mpi grompp -f minim.mdp -c last.2_solv_ions.gro -p topol.top -o em.tpr
mpirun -np 16 gmx_mpi mdrun -v -deffnm em

gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
mpirun -np 16 gmx_mpi mdrun -deffnm nvt
gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
mpirun -np 16 gmx_mpi mdrun -deffnm npt
gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
mpirun -np 16 gmx_mpi mdrun -deffnm md_0_1

Samuel Coulbourn Flores 
Associate Professor
Computational and Systems Biology Program
Department of Cell and Molecular Biology
Uppsala University

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