#!/bin/bash
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.err
#SBATCH --nodes=1
#SBATCH --gpus=1
#SBATCH --ntasks-per-node=1
#SBATCH --partition=gpu-shared
#SBATCH -t 0-00:20:00
#SBATCH --no-requeue
#SBATCH --reservation=amber24gpu
#SBATCH --account=gue998

Base=${1}
Parm=${1}.parm7


mdin=mdins/11_Production_0.5ns.mdin

module load workshop/amber24/default

newname=""

if [[ $Base == *-run-* ]]; then
  prefix=${Base%-*}    # Extract the part before the last hyphen
  suffix=${Base##*-}   # Extract the part after the last hyphen
  if [[ $suffix =~ [0-9]+ ]]; then
    number=${suffix#*-}   # Extract the numeric part after the second hyphen
    new_number=$(printf "%02d" $((number + 1)))  # Increment the number and pad with leading zeros if needed
    newname="${prefix}-${new_number}"
  else
    newname="${Base}-01"
  fi
else
  newname="${Base}-01"
fi

path=`pwd`

exe=${AMBERHOME}/bin/pmemd.cuda_SPFP


$exe -O -p ${Parm} -c ${Base}.rst7 -i ${mdin} -o ${newname}.mdout -inf ${newname}.mdinfo -x ${newname}.nc -r ${newname}.rst7 -ref ${Base}.rst7