Create script

script

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+#!/bin/csh
+#
+
+# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.7
+#
+# This folder contains GROMACS formatted CHARMM36 force fields, a pre-optimized PDB structure, and GROMACS inputs.
+# All input files were optimized for GROMACS 2019.2 or above, so lower version of GROMACS can cause some errors.
+# We adopted the Verlet cut-off scheme for all minimization, equilibration, and production steps because it is 
+# faster and more accurate than the group scheme. If you have a trouble with a performance of Verlet scheme while 
+# running parallelized simulation, you should check if you are using appropriate command line.
+# For MPI parallelizing, we recommand following command:
+# mpirun -np $NUM_CPU gmx mdrun -ntomp 1
+
+set init = step3_input
+set mini_prefix = step4.0_minimization
+set equi_prefix = step4.1_equilibration
+set prod_prefix = step5_production
+set prod_step   = step5
+
+# Minimization
+# In the case that there is a problem during minimization using a single precision of GROMACS, please try to use 
+# a double precision of GROMACS only for the minimization step.
+#mpirun -np 128 gmx_mpi grompp -f ${mini_prefix}.mdp -o ${mini_prefix}.tpr -c ${init}.gro -r ${init}.gro -p topol.top -n index.ndx -maxwarn 1
+#mpirun -np 128 gmx_mpi mdrun -v -deffnm ${mini_prefix} 
+
+
+# Equilibration
+#mpirun -np 128 gmx_mpi grompp -f ${equi_prefix}.mdp -o ${equi_prefix}.tpr -c ${mini_prefix}.gro -r ${init}.gro -p topol.top -n index.ndx
+#mpirun -np 128 gmx_mpi mdrun -v -deffnm ${equi_prefix}
+
+
+# Production
+set cnt    = 1
+set cntmax = 10
+
+while ( ${cnt} <= ${cntmax} )
+    @ pcnt = ${cnt} - 1
+    set istep = ${prod_step}_${cnt}
+    set pstep = ${prod_step}_${pcnt}
+
+	if ( ${cnt} == 1 ) then
+        set pstep = ${equi_prefix}
+        mpirun -np 128 gmx_mpi grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -p topol.top -n index.ndx
+	else
+        mpirun -np 128 gmx_mpi grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -t ${pstep}.cpt -p topol.top -n index.ndx
+	endif
+	mpirun -np 128 gmx_mpi mdrun -v -deffnm ${istep}
+	@ cnt += 1
+end