GROMACS

Envío de trabajo Gromacs :

Partiendo de los archivos :

folded-equil.ndx  folded-prod.gro  folded-test-protein.sh  folded.top  test-md-vv_prod_nvt.mdp

Ejemplo de script:

#!/bin/sh
#SBATCH -J bar-nvt-vv-fol
#SBATCH -o bar-nvt-vv-fol-%j.out
#SBATCH -p bifi                    # queue (partition)
#SBATCH -N 4                       # total number of nodes
#SBATCH --ntasks-per-node=24       # number of cores per node (maximum 24)


#### Cambiar según módulos necesarios para lanzar la versión de GROMACS que se desea testar
module add shared
module load openmpi/intel/1.10.2
module load intel/compiler/64/15.0.6/2015.6.233
module load gromacs/2018.4
ulimit -s unlimited
###################


COMMAND="mpirun -np $SLURM_NPROCS gmx_mpi mdrun"
NAME=folded

################## MAIN BODY #######################

echo -n "The simulation is running in: " > RUNNING_INFORMATION.info
echo $HOSTNAME >> RUNNING_INFORMATION.info
echo "Initial time: " >> RUNNING_INFORMATION.info
date >> RUNNING_INFORMATION.info

## Production step
gmx_mpi grompp -v -f test-md-vv_prod_nvt.mdp -po mdp_out.mdp -c ${NAME}-prod.gro -r ${NAME}-prod.gro -p ${NAME}.top -n ${NAME}-equil.ndx -o ${NAME}-nvt-vv.tpr -maxwarn 10

$COMMAND -s ${NAME}-nvt-vv.tpr -x ${NAME}-nvt-vv.xtc -c ${NAME}-nvt-vv.gro -o ${NAME}-nvt-vv.trr -e ${NAME}-nvt-vv.edr -nice 19 -v

gmx_mpi trjconv -f ${NAME}-nvt-vv.xtc -s ${NAME}-nvt-vv.tpr -o ${NAME}-nvt-vv_proc.xtc -pbc mol -ur compact -center <<EOF
1
1
EOF

gmx_mpi trjconv -f ${NAME}-nvt-vv_proc.xtc -s ${NAME}-nvt-vv.tpr -o ${NAME}-rot+trans_prot.xtc -fit rot+trans <<EOF
4
1
EOF

gmx_mpi covar -f ${NAME}-rot+trans_prot.xtc -s ${NAME}-nvt-vv.tpr -o eigenval.xvg -v eigenvec.trr -ascii covar.dat -xpm covar.xpm -b 0 -e 2000  <<EOF
4
1
EOF

echo "Final time: " >> RUNNING_INFORMATION.info
date >> RUNNING_INFORMATION.info

exit

Ejecución del script :

sbatch script.sh