[gmx-users] possible bug in posre
sergio.manzetti at fjordforsk.no
Wed Aug 30 16:53:43 CEST 2017
That means intercalation is affected directly by this, and the results will have no meaningful physical sense. Has anyone succssfully simulated intercalation in the DNA by some molecules without a method that disrupts the physicochemical energies of the DNA and the intercalator?
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From: "Justin Lemkul" <jalemkul at vt.edu>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Wednesday, August 30, 2017 4:50:55 PM
Subject: Re: [gmx-users] possible bug in posre
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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