[gmx-users] Help regarding applying constraint on individual molecule in a system

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 15:45:44 CET 2019

On 2/1/19 10:24 AM, anupama sharma wrote:
> Dear user's,
>      I need help regarding constraint. I am doing simulation of water (
> tip4p/2005) and carbon nanotube and want to put constraint only on carbon
> nanotube as after nvt simulation I had observed that carbon nanotube is
> getting deformed.

What you are looking for are restraints (biasing potentials to keep 
atoms near a fixed reference), not constraints (which fix bond lengths). 
gmx genrestr can generate a position restraint topology file.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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


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