[gmx-users] possible bug in posre
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!
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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.
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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