Run scripts, or jobfiles, contain all the necessary information to run a job.
An example is the mineq.sh script (thanks, Alice!). Doubly-commented parts
(##) are included here for explanation purposes.
To use this with as little modification as possible, copy your
whatever-random-name.inpcrd as whatever-random-name_init0.rst, and then
modify this script to change the #PBS -N line and change the
WT_protein_system_wat prefix in sys to match whatever-random-name.
#!/bin/bash ## Tell the script to run in a bash shell
#PBS -q my_cpu_alloc ## Use CPUs to run the job
#PBS -l nodes=1:ppn=20,mem=20GB ## Use 1 node, with 20 processors per node
## and 20GB memory
#PBS -j oe ## Combine standard output & standard error files
#PBS -r n ## Says the job is not rerunnable
#PBS -o err.error ## Write printed errors to a file titled err.error
#PBS -N WT_protein ## Name of the job to appear in queue
## Copy inpcrd to file named like WT_protein_system_wat_init0.rst7
sys=WT_protein_system_wat
prm=${sys}.prmtop
## Access the directory you submitted from
cd $PBS_O_WORKDIR
## Make a nodefile for all of the CPUs to communicate from
cat $PBS_NODEFILE > $PWD/PBS_NODEFILE
## Load the Amber module
module load amber/19-mvapich2
## Set counters for loop
e=0
f=1
## While file numbers less than 4, run this command
while [ $f -lt 4 ]; do
## Use 20 processors to use the parallel CPU pmemd amber code
## Use the respective mdin corresponds to the value of $f
## So loop 1 uses mdin.1 (etc, etc.)
## -o is your outfile, -p is your topology (prmtop)
## -c is your last save restart file, -r is the restart file written to
## -x is the velocity file written to, -ref is the reference (last restart file)
mpirun -np 20 -hostfile $PWD/PBS_NODEFILE $AMBERHOME/bin/pmemd.MPI -O \
-i mdin.$f \
-p ${prm} \
-c ${sys}_init$e.rst7 \
-ref ${sys}_init$e.rst7
-o ${sys}_init$f.out \
-r ${sys}_init$f.rst7 \
-x ${sys}_init$f.nc
## Update counters for loop
e=$[$e+1]
f=$[$f+1]
done