PLUMED might be useful in this case : http://www.plumed-code.org You could setup a simulation with http://plumed.github.io/doc-v2.0/user-doc/html/_u_p_p_e_r__w_a_l_l_s.html to achieve your goal. Or, as Justin suggested, it might be more straightforward for you to slightly modify the current Gromacs code. Sebastien > Date: Sat, 8 Mar 2014 08:32:37 -0500 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Using pull code to keep two monomers near each other > > > > On 3/7/14, 7:19 PM, Michael Daily wrote: > > Hi, > > > > I am trying to use the pull code to keep two peptide monomers near each > > other during a replica exchange simulation of (homo)dimerization. I do not > > want any bias if the COM distance between the two is less than some value > > r_max, as in umbrella sampling, i.e. > > > > E = 0 for r_ij <= r_max; > > E = k*(r_ij - r_max) for r_ij > r_max > > > > Can this be done with the pull code or some other function? Pull=constraint > > appears to essentially fix the COM distance, which I do not want to do > > either. > > > > There is presently no flat-bottom potential implemented in the pull code, but > one is planned for version 5.1. In the meantime, it should be relatively > easy > to add yourself, though, especially if you use a harmonic potential rather > than > a linear one beyond r_max, then it's just a very simple extension of the > existing harmonic potential. > > -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. -- Gromacs Users mailing list
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