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CHARMM

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Overview

CHARMM (Chemistry at HArvard Macromolecular Mechanics) is a general-purpose molecular mechanics, molecular dynamics and vibrational analysis package for modelling and simulation of the structure and behaviour of molecular systems.

Accessing CHARMM

Acquiring a Licence

CHARMM is licenced software, and users of the code should visit the Licence Page of the CHARMM website for information on how to acquire one.

If you already have a licence and would like to use CHARMM on HPCx, please contact the HPCx Helpdesk in order to be added CHARMM group on HPCx, which will allow you access to the binaries.

General Usage

There are a number of different binaries on HPCx, corresponding to different versions of CHARMM. The binaries can all be found in the directory:

/usr/local/packages/charmm/

For general usage, it is suggested you run the binary:

/usr/local/packages/charmm/c32b1/exec/ibmaixmp/charmm

This is the binary for CHARMM version 32b1, currently the most up-to-date on the system. This is a parallel binary and so will need to be invoked with poe.

Mixed Quantum Mechanical / Molecular Modelling (QM/MM)

It is possible to run mixed QM/MM calculations with CHARMM, by using GAMESS-UK to calculate the Quantum Mechanical contributions to the energy.

An earlier version of CHARMM (32a1) has been compiled for this purpose and can be found in the folder:

/usr/local/packages/charmm/c32a1_neb/exec/ibmaixmp/charmm

This version of the code incorporates an improved version of the Nudged Elastic Band (NEB) method code for optimising a number of images on a reaction path simultaneously.

Some sample files for replica path/NEB calculations can be found in the folder:

/usr/local/packages/charmm/c32a1/neb_test_cases

Further information