[gmx-users] Free volume variation during the simulation

[Mohamed Abdelaal]

I started with NVT then NPT then md production run.

Thanks,
Kohamed

On Wed, May 6, 2020 at 10:40 Arun Srikanth <askforarun at gmail.com> wrote:

> Is it an NPT simulation or NVT simulation?
> Arun
>
> On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, <m.b.abdelaal at gmail.com>
> wrote:
>
> > 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
> > > --
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