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From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@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, Se
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?
://www.phap.no/ | FAP ]
From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@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
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
;gmx-us...@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.
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
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,
