[gmx-users] Free volume variation during the simulation

[Mohamed Abdelaal]

Yes I measured both, the density and the free volume using gromacs.

Since the free volume changes with respect to time, shouldn’t the density
also change with time ?

Thanks,
Mohamed

On Wed, May 6, 2020 at 08:23 David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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.
> http://virtualchemistry.org
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>