[gmx-users] possible bug in posre

Sergio Manzetti 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? 

Sergio Manzetti 

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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 
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 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 


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