[gmx-users] Position Restraint for production MD

[Mark Abraham]

Hi,

What Justin said, and please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Mon, 14 Aug 2017 14:05 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/14/17 7:48 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I want to apply position restraints onto a bond for production MD, so
> that my protein does not go outside the simulation box during the MD run.
> Is this possible? And if so how would I go about doing this? Your
> suggestions will be much appreciated.
>
> Restraints are applied to atoms, not bonds.  There is also no such thing
> as "outside" a periodic box so there is no problem that you need to
> solve in this way.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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