[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water

André Farias de Moura moura at ufscar.br
Wed Mar 23 20:09:29 CET 2011

Hi Chris,

recently one of my students made a mistake during the model system assembling,
setting the initial volume to a value three times larger than expected
by the density.

after 1 microsecond (coarse grained MD, of course) there were droplets
and vacuum
between them, and the volume did not shrink until we applied a 100 bar
pressure to
the external bath (using Berendsen's weak coupling with the default
setting for the
Martini FF).

on the other hand, recently I was trying to model the methanol gas
phase using the
OPLS-AA FF and I found out it was a very tricky kind of model, as
different systems
with different volumes but the same (gas phase) density yielded quite
different results,
ranging from only one droplet (smaller system) to a distribution with
more than 99% of
monomers (larger system). from my standpoint, what happened to the
smaller systems
should be regarded as an artefact due to finite size of the system,
thus only the results
for the larger system got published, as I was not interested in the
discussion of the
artefact itself.

best regards,


On Wed, Mar 23, 2011 at 3:48 PM, Patrick Fuchs
<patrick.fuchs at univ-paris-diderot.fr> wrote:
> Hi Chris,
> I experienced the same kind of thing. In the process of building a box of
> liquid (organic solvent), at some point I wanted to get rid of a layer of
> vacuum around my system. So for shrinking the box I used similar settings as
> you and found also that the collapse was going slower than I'd have
> expected.
> One solution to accelerate this (if your goal is to shrink the box) is to
> increase the pressure (to say 100 atm). But it's important to stop the
> simulation in time (i.e. once the layer of vacuum has disapeared) otherwise
> the system shrinks too much and density is off.
> So to come back to your system which has a very big layer of vacuum around,
> and according to my experience, the volume is probably decreasing but too
> slowly to see anything signigicant (compared to the initial value) in 200 ps
> .
> Ciao,
> Patrick
> Le 21/03/2011 16:53, chris.neale at utoronto.ca a écrit :
>> Dear users:
>> I recently came across a system that was composed of tip4p water vapor
>> droplets separated by vacuum. This system is what you might get if you
>> did a NVT simulation of water with a box that was 10 times too large for
>> the number of water molecules.
>> I was surprised to see that this system did not collapse to any
>> significant extent during 200 ps of NPT equilibration at 1 atm using the
>> Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic
>> cut-off. (We also tried a number of other integrator/pressure coupling
>> combinations with the same results).
>> I had assumed that such collapse would occur quite rapidly. This does
>> not seem to be the case (no noticeable contraction within 200 ps).
>> Has anybody else done anything like this? Can anybody comment on their
>> expectations/experience of collapse from the gas state to the liquid
>> state under standard NPT conditions?
>> Thank you,
>> Chris.
> --
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> Dynamique des Structures et Interactions des Macromolécules Biologiques
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