[gmx-users] Free volume variation during the simulation

David van der Spoel spoel at xray.bmc.uu.se
Wed May 6 08:23:45 CEST 2020

Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal:
> Hello everybody,
> I have two fundamental questions please.
> I have measured the fee volume and I discovered that, the free volume
> changes with respect to the time during the production run (different value
> for each frame). However I have measured the density but the result does
> not change with respect to time.
> Shouldn't the density also changes with time if the free volume changes
> with  time ?
> I also can't understand why the free volume changes with respect to the
> time, if the number of molecules and volume of box didn't change.
> Many Thanks,
> Mohamed
This is due to atomic fluctuations, that is they overlap more or less 
depending on their distance, Did you use the freevolume tool in gromacs? 
It may also depend on whether each freevolume calculations is converged 
(-ninsert option).

David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.

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