First thanks for the answers. I checked several sections of the
trajectory, but the deviation is always the same, even when disregarding
the first 500 ps or looking only at the last 500 ps of the trajectory
where everything is nice equilibrated. I think the error is
insignificantly small (however, the value was reported in this precision
in the original paper) but I was interested in possible reasons of this
behavour, e.g. numerical errors or different treatment of certain
interaction parameters between Gromacs and Gromos (in my studies I
usually work with both programs).
There is another question that could possibly be answered by Berk: I
often use his Orientation Restraints algorithm implemented in Gromacs.
While all results are fine and most of the analysis parameters of an
RDC- driven run are clear to me, I am not sure of the meaning of the
g_energy output "Orient.-Rest." and "Ori.-R.-RMSD". Are these analysis
parameters some kind of energy terms like the
restraining potential or is the output given in Hertz and what do they
actually mean?
Thanks in advance for any help,
Andreas
Xavier Periole wrote:
On Wed, 12 Mar 2008 12:24:02 +0100
Berk Hess <[EMAIL PROTECTED]> wrote:
Hi,
Did you make your DMSO molecule completely rigid?
Should we really worry about such a difference in density?
(1095-1108)/1095=0.012
How precise is the value reported? Did you estimate the error
by using different sections of the trajectory?
Berk.
Date: Wed, 12 Mar 2008 12:18:08 +0100
From: [EMAIL PROTECTED]
To: [email protected]
Subject: [gmx-users] DMSO G53a6 FF in Gromacs
Dear Gromacs Users,
I simulated the preequilibrated box of DMSO that is located in the
Gromacs Force Field Distribution with the G53a6 Gromos FF parameters
(adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)).
After temperature equilibration I performed a NPT run but in
contrast to the reported density of 1095 kg m-3 I always get values
around 1108 kg m-3. I used berendsen pressure coupling as well as
reaction field for treating long-range interactions with 0.8 / 1.4
cut-offs.
I looked through the Gromacs archive but couldnt find an answer for
this problem. Has anyone an idea what could be the reason for this
result?
Thanks for any comments!
Best regards,
Andreas
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XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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