###### tags: `software` # Charmm quick usage guide ## Description A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models. ## Single Node Multiple CPU * #### STEP1 Download the submission script Please refer to the following script (charmm_sn.sh) ```export CWD=`pwd` ``` ```cp /opt/ohpc/Taiwania3/pkg/chem/charmm/charmm/submit_script/charmm_sn.sh $CWD``` * #### STEP2 Change your wallet account ```sed 's/JOB_ACCOUNT/XXXXXX/' charmm_sn.sh``` XXXXXX 填入計畫帳號 * #### STEP3 Choose the number of nodes and the number of processes * Modification Part 1 ``` #SBATCH -n 56 # Number of MPI tasks (i.e. processes) #SBATCH -c 1 # Number of cores per MPI task #SBATCH -N 1 # Maximum number of nodes to be allocated ``` * #### STEP4 Prepare your input files * Copy a example ``` cp -r /opt/ohpc/Taiwania3/pkg/chem/charmm/testcase/example/basic ./ ``` * Upload your own testcase * #### STEP5 Submit the job and execute ``` sbatch charmm_sn.sh ``` ### charmm_sn.sh ``` #!/bin/bash #SBATCH -A JOB_ACCOUNT # Account name/project number #SBATCH -J charmm_sn # Job name #SBATCH -p ctest # Partiotion name #SBATCH -n 56 # Number of MPI tasks (i.e. processes) #SBATCH -c 1 # Number of cores per MPI task #SBATCH -N 1 # Maximum number of nodes to be allocated #SBATCH -o charmm_sn.out # Path to the standard output file #SBATCH -e charmm_sn.err # Path to the standard error ouput file # module load module load compiler/intel/2020u4 module load IntelMPI/2020 # module load charmm module load chem/charmm/c47b1 export APPROOT=$HOME/basic echo '=======================================================' cd $APPROOT mpirun -n 56 charmm -i tutorial.inp >& file.out ```