Thank so much Justin for the help, I am going to reinstall gromacs 5 and try, I decided to install gromacs 4.6.5, and instead of a flat bottom potential , uses position restraint in x and y , in order to get the pmf of a drug passing throughout of an ion channel , I don't know if this could affect that much due to this bias(do you think so?) , but If I have time try to get both using gromacs 5 ,
Thanks again Andrés Ortega Ing. Electrónica Universidad del Valle El 7/04/2014, a las 20:45, "Justin Lemkul" <[email protected]> escribió: > > > On 4/4/14, 10:48 AM, Andres Ortega Guerrero wrote: >> Thank you Justin, >> >> I will appreciate the help with this doubt, of the reference group, that is >> not 0 , is 26 in the index file, >> or the appropiate definition of the reference group thanks > > I want to revisit this because I am now working through it myself. What was > not immediately clear is that these indices do not, in fact, have anything to > do with the order of the index file. Instead, the indices correspond to the > groups used in pulling. > > Since the pull code is now more general, such that multiple reaction > coordinates can now be defined (and thus more than one reference group), one > must specify the number of reaction coordinates (pull-ncoords), how many > groups total are involved in any sort of reaction coordinate (pull-ngroups), > and then identify which of those groups are participating in each of the > reaction coordinates. > > The simplest case is to use the biasing potential along one reaction > coordinate with two groups. Therefore: > > pull-ngroups = 2 > pull-ncoords = 1 > pull-coord1-groups = 1 2 > pull-group1-name = refgroup > pull-group2-name = pullgroup > > I have that much working at this point. One could, in theory, then extend > the situation to have two reaction coordinates between 3 or 4 groups, i.e. > > pull-ngroups = 3 > pull-ncoords = 2 > pull-coord1-groups = 1 2 > pull-coord2-groups = 1 3 > pull-group1-name = refgroup > pull-group2-name = pullgroup1 > pull-group3-name = pullgroup2 > > I assume that will work (famous last words, but I have no time or need to > test that setup at the moment). What it is intended to do is apply a biasing > potential between groups 1 and 2, and 1 and 3 simultaneously. > > -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 > > [email protected] | (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 [email protected]. -- 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 [email protected].
