[gmx-users] DMSO G53a6 FF in Gromacs

[Xavier Periole]

On Wed, 12 Mar 2008 12:24:02 +0100
  Berk Hess <gmx3 at hotmail.com> 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: andreas.frank at ch.tum.de
>> To: gmx-users at 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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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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