[gmx-users] Free volume variation during the simulation

[David van der Spoel]

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 <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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-- 
David van der Spoel, Ph.D.,
Professor of Biology
Uppsala University.
http://virtualchemistry.org