On 11/18/14 10:38 AM, Adriana Garro wrote:
Dear gromacs users, I am working in a system composed by a protein in a solvated box. It is a coarse-grained model (Martini ff). The protein has an amyloid part (strand-loop-strand), at first I tried to simulated this without restraints but the structure collapsed, then I used position restraints as a result it kept the structure but due to the type of restraint I applied it is fix in the box without possibility of motion (translate, rotate). I was reading and maybe using dihedral restraints I can solve this problem. Someone knows if it is possible?
Sure it is. See manual section 4.3.4 and Table 5.5. There's an online how-to at http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints but it may be outdated. See if it works (the manual seems to indicate that it is easier than what is stated there) and please suggest changes if it doesn't!
-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.
