[gmx-users] possible bug in posre

[Sergio Manzetti]

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? 


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 3:43:09 PM 
Subject: Re: [gmx-users] possible bug in posre 

On 8/30/17 9:33 AM, Sergio Manzetti wrote: 
> Weird stuff, because the 1 simulation turned out well, even without POSRE. 
> 
> Can this POSRE be reliable, in terms of intercalation of molecules? In other words, does the energy that is imposed by POSRE really reflect the energy landscape of the bonds simulated in the remaining of the molecules in the box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then any intercalation study is really futile! 

You're talking about both constraints and restraints here, and typically 
restraints are applied to non-H atoms and constraints involve bonds to H 
atoms. Restraints are biasing potentials to prevent motion. You'll 
have to explain what you're studying and why you think you need 
restraints (which are typically only used during equilibration). 
Restraints are artificial, so anything that comes out of a restrained 
simulation should be interpreted with care, because you could be 
completely preventing relevant dynamics. Binding of a molecule to a 
restrained target may be completely unphysical. 

-Justin 

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Justin A. Lemkul, Ph.D. 
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Virginia Tech Department of Biochemistry 

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