[gmx-users] Re: Update on virial calculation non consistant

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 7 09:31:24 CET 2006

Tandia, Adama wrote:
> Dears,
> Thank you David for your help. I would like to report my new findings.
> Used NVT annealing from 3000K to 1000K during 2 ns.
> Calculated Virial from Eq. 3.16 and 3.18 of Manual 3.2. No consistency:
>         * two virial curves with very different slopes

Did you compute them yourself by adding code?

> Extended the NVT run with an NVT at 1000K for 500ps and recalculate 
> Virial from (3.16) and (3.18)
> Found a multiplying factor of 2 between Eq (3.16) and (3.18) to have a 
> match between the two virial values.

> Questions:
>         1: How can we explain the results in the first case?
>         2: If any, which one of the two equations is correctly implemented?
> I thank you in advance for your prompt answer.

There are many different factors playing in. There are contributions to 
the virial from constraints and from PME, if  you use any of these. From 
the information you give it is not possible to deduce:
1. whether there is any inconsistency
2. if so, how to explain it.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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