[gmx-users] CHARMM-GUI: new features for GROMACS
jalemkul at vt.edu
Tue Oct 21 14:21:28 CEST 2014
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
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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