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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