Talk:Mod:Hunt Research Group/ChemShell Introduction

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:

module load chemshell/3.5.0

The interactive mode is then invoked by entering chemsh.x. Alternatively, you can run scripts via the command:

chemsh.x NAME_OF_SCRIPT

where NAME_OF_SCRIPT is the name of script containing the ChemShell commands you want to run.

Submitting via the Portable Batch System (PBS)

To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load chemshell/3.5.0
module load intel-suite mpi

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/

The command module load chemshell/3.5.0 loads the ChemShell module as explained above. The command module load intel-suite mpi loads the modules which will allow you to run calculations employing more than one processor.

You will also have to load modules of the QM or MM codes that you intend to use during the calculation.

The following cp commands copies all the input files into the temporary directory ($TMPDIR) for running the calculation.

The command mpiexec chemsh.x energy.chm > energy.out instructs ChemShell to execute the script called energy.chm and to write any standard output into energy.out.

The final cp command copies all output files (includes energy.out along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:

qsub NAME_OF_SCRIPT

where NAME_OF_SCRIPT is the name of the script.