[gmx-users] Re: Different system volumes from gromacs versions 3.2.1 and 3.3.1

Xavier Periole X.Periole at rug.nl
Tue Jan 8 15:56:15 CET 2008

On Tue, 8 Jan 2008 15:39:51 +0200 (EET)
  Perttu Niemela <perttu.niemela at hut.fi> wrote:
> Hi All,
> In December here was a short discussion about a water system, for which 
>gromacs versions 3.2.1 and 3.3.1 produced different average volumes. I have 
>experienced similar thing with Marrink's coarse grained water (about 1500 
>beads in the box), but to opposite direction.

Just by curiosity: which version the ff you use?

> My test runs with gromacs 3.1.4 and 3.2.1 always give a larger average 
>volume than versions 3.3.1. and 3.3.2. The difference is much larger than the 
>fluctuations. I use berendsen barostat (isotropic; p = 1 atm) and thermostat 
>(T=300K). In my simulations, the off-diagonal terms of the virial are very 
>close to zero. Additionally, I have tested using simple cutoffs instead of 
>switch/shift functions, but it does not affect the general conclusion.

How much is the difference you observe and which percentage of the volume
does this represent?

> Can it be that the difference in calculating the kinetic energy (and 
>temperature) leads to the observed volume difference? I did a quick test to 
>modify the code of gromacs v. 3.3.1 such that it calculates kinetic energy 
>exactly like in v. 3.2.1, and the volume jumps back up.
> Can somebody please confirm, if this is expected? I cannot fully understand 
>how a more exact calculation of the kinetic energy would lead to a 
>significant change of the average volume (?)

Well a change in temperature should affect the volume of course, so the
change in estimation of the kinetic energy will affect the volume but
the effect should be very small!


> Regards,
> Perttu Niemela
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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