[gmx-users] possible bug in posre

Sergio Manzetti sergio.manzetti at fjordforsk.no
Wed Aug 30 15:40:28 CEST 2017

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! 

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 3:35:48 PM 
Subject: Re: [gmx-users] possible bug in posre 

On 8/30/17 9:21 AM, Sergio Manzetti wrote: 
> Hi, I have made 5 copies of a simulation, using the following mdp , with gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the DNA strands fly everywhere in the box, outside the box and even double up in longitude direction. All the directories are identical in their files, and the grompp has been used respectively. Does this sound familiar to some, or is it most likely a grompp error? This is the second time I try this. 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 

The fact that there's no -DPOSRES here suggests you're probably not 
actually using restraints. Therefore, what you're seeing is your DNA 
diffusing across the box and experiencing the normal PBC imaging 
effects. If restraints are on, you'll see a corresponding energy term 
in the .log and .edr files. If it's not there, there are no restraints. 



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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