Add files via upload

md.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+#SBATCH --time=36:00:00
+#SBATCH --nodes=40
+#SBATCH --ntasks-per-node=32
+#SBATCH --constraint=haswell
+#SBATCH --qos=regular
+#SBATCH --account=m906
+#SBATCH --job-name=full-md
+
+module load gromacs/2020.2.hsw
+
+echo "Start at `date`"
+
+# continue GROMACS MD production
+
+srun -n 1280 mdrun_mpi_sp -deffnm md -maxh 36.00 -cpi -multidir 1 2 3 4 5 &
+
+wait
+
+echo "End at `date`"
+

nvt-md.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+#SBATCH --time=36:00:00
+#SBATCH --nodes=40
+#SBATCH --ntasks-per-node=32
+#SBATCH --constraint=haswell
+#SBATCH --qos=regular
+#SBATCH --account=m906
+#SBATCH --job-name=full-nvt-md
+
+module load gromacs/2020.2.hsw
+
+echo "Start at `date`"
+
+# prepare executables for NVT equilibration for 5 instances
+
+for ((i=1;i<=5;i+=1))
+do
+cd $i
+srun -n 1 gmx_sp grompp -f ../nvt.mdp -c emin.gro -r emin.gro -n ../full.ndx -p ../full.top -o nvt.tpr > grompp-nvt.log &
+cd ../
+done
+
+wait
+
+# run GROMACS NVT equilibration
+
+srun -n 1280 mdrun_mpi_sp -deffnm nvt -maxh 36.00 -cpi -multidir 1 2 3 4 5 &
+
+wait
+
+# prepare executables for NPT equilibration for 5 instances
+
+for ((i=1;i<=5;i+=1))
+do
+cd $i
+srun -n 1 gmx_sp grompp -f ../npt.mdp -c nvt.gro -r nvt.gro -n ../full.ndx -p ../full.top -t nvt.cpt -o npt.tpr > grompp-npt.log &
+cd ../
+done
+
+wait
+
+# run GROMACS NPT equilibration
+
+srun -n 1280 mdrun_mpi_sp -deffnm npt -maxh 36.00 -cpi -multidir 1 2 3 4 5 &
+
+wait
+
+# prepare executables for MD production for 5 instances
+
+for ((i=1;i<=5;i+=1))
+do
+cd $i
+srun -n 1 gmx_sp grompp -f ../md.mdp -c npt.gro -n ../full.ndx -p ../full.top -t npt.cpt -o md.tpr > grompp-md.log &
+cd ../
+done
+
+wait
+
+# run GROMACS MD production
+
+srun -n 1280 mdrun_mpi_sp -deffnm md -maxh 36.00 -cpi -multidir 1 2 3 4 5 &
+
+wait
+
+echo "End at `date`"
+

run.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+ID=$(sbatch --parsable nvt-md.sh)
+
+for ((i=1;i<=5;i+=1))
+do
+ID=$(sbatch --parsable --dependency=afterany:$ID md.sh)
+done
+