Dear Gromacs Users,
I am simulating a Membrane protein, the extracellular domain alone (since the
structure of only extracellular domain is solved). So I will have to simulate
the protein in such a way that only the translational motion is allowed but the
rotational motions are prevented
nahren manuel wrote:
Dear Gromacs Users,
I am simulating a Membrane protein, the extracellular domain alone
(since the structure of only extracellular domain is solved). So I will
have to simulate the protein in such a way that only the translational
motion is allowed but the rotational
a good idea ? similar to what one would do
in membrane simulation.
Best,
nahren
--- On Thu, 11/11/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Translation motion during MD
To: Discussion list for GROMACS users gmx-users@gromacs.org
semiisotropic is fine.
-Justin
Best,
nahren
--- On *Thu, 11/11/10, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Translation motion during MD
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday
Hi, all:
I am running dynamics with PBC in xyz direction. Now I got a problem.
Since PBC is applied, some atoms will move to the other side of the box and
this will change the polarization. I need the results of polarization, so I
do not hope that the polarization changed during the dynamics.
Dear All,
I really apologize for asking a peptide translation related question again. I
have a lipid-peptide system and I have already carried out the production run
for 20ns. The peptide has moved towards one of the edges (I didnt specify
comm-grps in the mdp file). I have to translate the
priyanka srivastava wrote:
Dear All,
I really apologize for asking a peptide translation related question
again. I have a lipid-peptide system and I have already carried out the
production run for 20ns. The peptide has moved towards one of the edges
(I didnt specify comm-grps in the mdp
Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, 12 August, 2008 12:05:26 AM
Subject: Re: [gmx-users] translation
priyanka srivastava wrote:
Dear All,
I really apologize for asking a peptide translation related
Selected 1: 'Protein'
Select group for output
System
I am using 3.3.3.
thnx,
Priyanka..
- Original Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, 12 August, 2008 12:05:26 AM
Subject: Re: [gmx-users] translation
list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, 12 August, 2008 1:15:00 AM
Subject: Re: [gmx-users] translation
priyanka srivastava wrote:
Dear Justin,
Thanks a lot for replying back.
These are the two things that I have tried but still the peptide does
not come at the center
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