[gmx-users] Position Restraint for production MD

[Justin Lemkul]

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.
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Virginia Tech Department of Biochemistry

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