Dear Justin: Many thanks for your reply. I would like to test the new feature, but I have no much spare time recently. So it seems that I have to choose some atoms from the two chains seperately, and do distance restraint on these atoms.
Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn <wt...@biophy.nju.edu.cn>* On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/5/15 2:39 AM, WT Ren wrote: > >> Dear Gromacs Users, >> >> I am trying to apply a distance restraint between two chains' center of >> mass to prevent them diffusing far away from each other. As I known, the >> pull code seems only can restrain the distance to a reference distance >> with >> harmonic potential, while the distance restraint seems can not be >> applied >> to center of mass. >> >> So can anyone help on this issue? >> >> > I am assuming that you want to apply some sort of flat-bottom potential, > to be applied only when the chains move a certain distance. Indeed the > pull code cannot do that at present, but a flat-bottom potential is in > development if you want to test it: > > https://gerrit.gromacs.org/#/c/3947/ > > -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.
