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: gmx-users@gromacs.org
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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