[gmx-users] possible bug in posre

[Justin Lemkul]

On 8/30/17 10:39 AM, Sergio Manzetti wrote:
> Its only the constraints in DPOSRE that I am concerned about. They do keep the antisense and the sense strands together, however, do they keep this together so that also intercalation between the bases is not any longer physically related?

Constraints and restraints are different; -DPOSRES has nothing to do 
with constraints.

Position restraints bias the positions of the affected atoms towards 
their reference coordinates.  They are absolute in space, so they don't 
"keep strands together" in the literal sense, but they simply 
prevent/disfavor anything from moving.

-Justin

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================