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

Patrick Fuchs patrick.fuchs at univ-paris-diderot.fr
Wed Mar 23 19:48:45 CET 2011

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 .


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.

!!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31
Web Site: http://www.dsimb.inserm.fr/~fuchs

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