When you got an account on CDAC, they must have attached a pdf that would help you understand how one can use the HPC. In addition, you might want to look at the manual of the respective supercomputing facility to run your codes. I am not sure what is currently being used but when I was using PARAM YUVA, I was probably using PBC script to submit my jobs. The PBS script looked somewhat like below:

#######################################################

#!/bin/bash

#PBS -l nodes=1:ppn=16

#PBS -l walltime=02:00:00

#PBS -q batch

#PBS -e err_""$PBS_JOBID

#PBS -o out_""$PBS_JOBID

##PBS -m bae

#PBS -r n

#PBS -V

export I_MPI_JOB_CONTEXT=$PBS_JOBID

echo PBS JOB id is $PBS_JOBID

echo PBS_NODEFILE is $PBS_NODEFILE

echo PBS_QUEUE is $PBS_QUEUE

NPROCS=`wc -l < $PBS_NODEFILE

echo NPROCS is $NPROCS

cd $PBS_O_WORKDIR

mpirun -np 16 /opt/gromacs-4.5.4/gromacs-4.5.4-mpi/bin/mdrun_mpi -s r512pr.tpr -o r512_eq.trr -c r512cf3so3pr.gro

#################################################################################

All the best.

They will provide all the information including scripts and manual. If you have further question direct it to the mailing ide they provided.

Most HPC facilities provide template scripts, but not help with specific applications. Breaking the task into two or more parts, start with learning how to use the cluster. It is relevant to know its architecture. Then from your applications specific users, you can find how to do the simulations. It may help if you go to other departments and talk to advanced grad students/post-docs. good luck.