[gmx-users] possible bug in posre

[Sergio Manzetti]

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 

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