On 8/13/14, 10:45 AM, Alex s wrote:
I should've mentioned that the those snapshots are of different system set ups. The first snapshot is for a system I set up by doubling the size of lipid box and placing the polymer just above the membrane. The second
A little context next time, please.
snaphshot is for a another system where I left the lipid box size as it was after equilibration and placing the polymer above the membrane. The only strange thing that I notice is the polymer is being almost 'repelled' by the
That sounds like a force field problem. What is the source of your parameters?
bilayer. Also is there an easy way to automatically fill the empty spaces in the box with water? The way I do it is quite tedious where I have to manually edit water boxes and position them to fill the empty space in the system
That's what genbox (gmx solvate in 5.0) is for. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
