Thank you very much. I really appreciate it. On Sun, Mar 26, 2017 at 6:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote: > >> Hi all, >> >> I have a system in which I need to maintain the center of mass distance >> between two molecules constant for an umbrella window. The structures are >> not strictly aligned along an axis as they are the product of an >> equilibrium simulation.I have the following code. >> >> pull = umbrella >> pull_ngroups = 2 >> pull_group1_name = molecule1 >> pull_group2_name = molecule2 >> pull_coord1_type = umbrella >> pull-geometry = distance >> pull_coord1_groups = 1 2 >> pull-dim = Y N N >> pull_coord1_rate = 0.0 >> pull_coord1_k = 2000 >> >> I have the following questions. >> >> 1) Does pull-dim = Y N N mean that the k=2000 is applied along the x >> coordinates only in maintaining the distance constant? >> >> > Yes. > > 2) If I want to apply a harmonic potential to maintain the distance along >> both x and y axis constant (in maintaining the distance *r* constant) do I >> have to make the following changes? >> >> pull_coord2_groups = 1 2 >> pull-dim = Y Y N >> pull_coord2_k = 2000 # this is applied on the y coordinate (that is the >> picture I have in my mind) >> >> > No. You have one biasing potential that acts along x and y. The biasing > force is applied based on the distance calculated along those two axes, not > independently in x and y. > > -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. > -- 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.