[gmx-users] Position Restraint for production MD

Justin Lemkul jalemkul at vt.edu
Mon Aug 14 14:04:49 CEST 2017

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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