Thanks Justin! I will try right now. Best, Adriana
*********************************************************** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..............:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ********************************************************** 2014-11-18 20:18 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > 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 but it may be outdated.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. > -- 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.