[gmx-users] CHARMM-GUI: new features for GROMACS

Justin Lemkul jalemkul at vt.edu
Tue Oct 21 14:21:28 CEST 2014

Hi All,

I am pleased to announce that the CHARMM-GUI team has extended the capabilities 
of CHARMM-GUI (www.charmm-gui.org) to provide GROMACS topologies, .mdp files, 
and run scripts as part of the standard output of CHARMM-GUI.  That is, one can 
now assemble a system (even heterogeneous membranes with embedded proteins) 
using CHARMM-GUI and immediately proceed to minimization and dynamics - no more 
tedious separation of water or other components to input into pdb2gmx! 
Everything you will need is in the "gromacs" subdirectory of the downloaded 
tarball.  The input files assume you are using version 5.0 or higher.

The .mdp files have been compared against the CHARMM program and have been found 
to yield equivalent forces, so you can be assured that these are the correct 
settings to be used with the CHARMM36 force field.  The equilibration protocol 
for membrane systems (please see the README file in the downloaded tarball) has 
been highly optimized to gently relax the system for maximum stability.

We hope that these new features will streamline your workflows and make the 
construction of complex systems even easier.  If there are any questions or 
comments, please send them to the CHARMM-GUI team via the email link at 

Happy simulating!



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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