On 4/5/16 9:29 AM, Michał Kadlof wrote:
Hello, I would like to run my simulations inside closed sphere. It may be something like soft-walls potential (0 inside a sphere, and proportional to r^2 outside sphere with force directed to the center of sphere) or something similar. Is it possible with Gromacs? I'm not afraid to mess up with a Gromacs code a little bit if it necessary.
Flat-bottom position restraints will do this.
I'm also curious if it possible to add harmonic interaction between arbitrary chosen two beads in simulations. I would also like to define different interaction constant for each such spring separately.
Use the pull code. In version 5.1 there is the ability to define as many such interactions as you like.
-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.
