CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is 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 A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Installed versions

CHARMM (Developmental Version 47b3, March 1, 2023)

CHARMM manual can be downloaded from here: `https://www.academiccharmm.org/documentation/version/c47b2>`_

Submitting a CHARMM calculation

This module load command is needed once per session:

module load charmm

To demonstrate the CHARMM job submission, the steps and the four necessary files are given below for a minimalistic CHARMM minimization calculation

The CHARMM input file wat5_mtip3p.inp:

* 5-water cluster with CHARMM mTIP3P
* Read coordinates from wat5_start.pdb, minimize, write out
*

BOMLEV -2
PRNLEV 5

! 1) Load official water+ions toppar (must be in current directory)
stream toppar_water_ions.str

! 2) Define a 5-water system (TIP3)
read sequence TIP3 5
generate WAT setup

! 3) Read coordinates from PDB
open unit 10 read form name wat5_start.pdb
read coor pdb unit 10 resid
close unit 10

! Quick sanity check: should NOT see 9999 in statistics
coor stat sele all end

! 4) Nonbonded setup (vacuum cluster, no PBC)
set CUTNB  = 18.0
set CTOFNB = 16.0
set CTONNB = 14.0

nbonds atom vatom vswitch cutnb @CUTNB ctofnb @CTOFNB ctonnb @CTONNB -
       eps 1.0 e14fac 1.0

update
energy

! 5) Energy minimization
cons harm force 1.0 sele segid WAT end
mini abnr nstep 500 nprint 50
mini abnr nstep 1500 tolg 0.01 nprint 50

cons harm none
mini abnr nstep 1000 tolg 0.01 nprint 50

energy

! 6) Write out PSF and coordinates
open unit 20 write form name wat5_mtip3p.psf
write psf card unit 20
close unit 20

open unit 30 write form name wat5_mtip3p.crd
write coor card unit 30
close unit 30

open unit 40 write form name wat5_mtip3p.pdb
write coor pdb unit 40
close unit 40

stop

The necessary coordinate (wat5_start.pdb) and topology and parameter information (toppar_water_ions.str) files can be accessed from here:

wat5_start.pdb
toppar_water_ions.str
Job script for a regular CHARMM SLURM job (subCHARMM.sh):

#!/bin/bash
#SBATCH --job-name=CHARMM
#SBATCH --output=wat5_mtip3p.%j.out
#SBATCH --error=wat5_mtip3p.%j.err
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:05:00
#SBATCH --partition=cpu

module load charmm
cd "$SLURM_SUBMIT_DIR"

/opt/software/packages/charmm/gnu/cpu/c47b2/bin/charmm < wat5_mtip3p.inp > wat5_mtip3p.log

Then to submit the CHARMM job via SLURM to the KOMONDOR gpu queue:

sbatch subCHARMM.sh

How to Cite CHARMM

If you use CHARMM in your research, please cite the following paper:

(1) B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus: CHARMM: The Biomolecular simulation Program, J. Comp. Chem. 30, 1545-1615 (2009), https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287

The original CHARMM reference and a brief update are:

(2) B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem. 4, 187-217 (1983) https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540040211

(3) A. D. MacKerell, Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus: CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, Vol. 1, 271-277, P. v. R. Schleyer et al., eds., John Wiley & Sons, Chichester (1998) https://onlinelibrary.wiley.com/doi/10.1002/0470845015.cfa007

Last update by Milán SZŐRI: 2025-12-08