Many thanks david for the explanation.

In did NVT then NPT equilibiration and then the production run, in the
production run .mdp file I have the same parameters as in NVT and NPT.mdp
files. Does this mean that my simulation is a NVT simulation or NPT ?

Is it possible to do only one of them (NVT or NPT) equilibiration ? I
thought that I must do both of them before I start the final production
run.

Thanks again,
Mohamed

On Wed, May 6, 2020 at 12:50 PM David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> Den 2020-05-06 kl. 10:21, skrev 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 ?
> What do you mean with "changes"? If the density is constant (with
> fluctuations) in an equilibrium NPT simulation then the free volume
> should fluctuate around an average as well.
>
> If you have a NVT simulation on the other hand, the total density is
> going to be constant, but if your system undergoes a phase change the
> freevolume will change.
> >
> > Thanks,
> > Mohamed
> >
> > On Wed, May 6, 2020 at 08:23 David van der Spoel <sp...@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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>
> --
> David van der Spoel, Ph.D.,
> Professor of Biology
> Uppsala University.
> http://virtualchemistry.org
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