[gmx-users] Dihedral restraints

[Justin Lemkul]

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be outdated.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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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