refactor: run mdprep.sh once before mdrun retry loop

mdprep.sh is idempotent (skips when production checkpoint exists), so
there's no reason to re-run it on every SIGABRT/SIGSEGV restart. Only
mdrun.sh needs to be retried.

Author: FridrichMethod

scripts/gromacs/mdrun/mdrun.sbatch

@@ -33,13 +33,15 @@ export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
 
 # If the checkpoint file for production exists, will skip the pre-processing step
 # and continue from the checkpoint file
+bash mdprep.sh
+
 attempt=0
 max_restarts=3
 
 while true; do
     attempt=$((attempt + 1))
     status=0
-    bash mdprep.sh && bash mdrun.sh || status=$?
+    bash mdrun.sh || status=$?
 
     if [[ $status -eq 0 ]]; then
         exit 0