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 www.charmm-gui.org
Happy simulating! -Justin -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
