[gmx-users] Dihedral restraints
jalemkul at vt.edu
Tue Nov 18 20:18:34 CET 2014
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be outdated.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 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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