On 9/16/14 9:15 PM, Kester Wong wrote:
Dear Justin, Thank you for the feedback. Yep, the converted structure is not any better than a starting configuration, i.e. discontinued ensemble velocitites and another energy minimisation for the converted structure is necessary. What I thought would be helpful is that for water droplet formation, users might save a couple of nanoseconds by having a droplet starting file, instead of a water box.
Anyone is welcome to contribute whatever they feel is useful in the User Contributions section of the website.
Conversions between polarizable and nonpolarizable models will be trivial when my Drude branch is ready to be merged into the main code repository, so the need for any hacks is very low. Soon it will be possible to very easily do full biomolecular simulations with polarizable force fields just as one would with additive models (i.e., pdb2gmx will build everything for you). There are a few lingering issues that I'm sorting out, but it should be done fairly soon.
-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.
