[gmx-users] Dihedral restraints

[Adriana Garro]

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...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com


**********************************************************

2014-11-18 20:18 GMT+01:00 Justin Lemkul <jalemkul at 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 but it may be outdated.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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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