[gmx-users] Help for using Lincs along with constraint
jalemkul at vt.edu
Mon Feb 4 15:49:44 CET 2019
On 2/3/19 10:00 AM, anupama sharma wrote:
> Dear user's
> I need help for using lincs along with constraint. I am doing water
> (tip4p/2005) and carbon nanotube simulation and since I am using
> tip4p/2005, I had used exclusion for rigid body dynamics and for that I
> kept lincs off. But after nvt simulation bonds in carbon nanotube is
> getting broken. What I can do for that.....
LINCS is not applied to water unless you are manually defining the
constraints (e.g. not using SETTLE).
You will have to define what you mean by "getting broken," because that
may simply be a PBC effect. Bonds are bonds. They don't break in an MD
simulation. Our ability to perceive them as the physics intends,
however, is another matter.
Justin A. Lemkul, Ph.D.
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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