On Thu, Nov 21, 2013 at 12:06 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> Mark, does it possible to do such for the ensemble (each frame from the > trajectory) at one step ? For example I need to perform umbrella sampling > in 50 windows extracted from the initial trajectory expanding in each > umbrella window the Z dimension and add water to it. > > I can't think of any way to do this in one step, but it's trivial to script. There is no getting around the fact that you need to perform multiple manipulations on multiple configurations. Keep in mind that the resulting structures may not be topologically identical (number of waters may vary) so you will need a corresponding topology for each configuration, anyway. -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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.
