[gmx-users] DMSO G53a6 FF in Gromacs

[Andreas Boozo Frank]

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 <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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