[gmx-users] possible bug in posre
jalemkul at vt.edu
Wed Aug 30 16:51:06 CEST 2017
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
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 A. Lemkul, Ph.D.
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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