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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Mar 23 21:06:10 CET 2011

Thanks Patrick and Andre!

We repeated this with a few box sizes just to get a quick handle on  
it. The equilibrium volume is about 64 nm^3. If we start with a volume  
of 1000 nm^3 then the overall box does not collapse at all within 200  
ps of NPT Langevin dynamics at 1 atm.If we start with a volume of 200  
nm^3, then it does collapse to approximately 64 nm^3 within 200 ps of  
such simulation.

My best guess is that the rapid collapse is driven by nonbonded  
interactions and thus the rapid collapse does not occur when the  
system is so large with such low density that water forms isolated  
vapour droplets that do not interact with each other by LJ  
interactions. Sure, it is expected to collapse eventually from the 1  
atm pressure coupling, and we have also observed that high pressure  
works, but at 1 atm it might take a very long time to reach equilibrium.

I agree with Andre that none of this matters to regular simulations as  
there is no good reason to go through this type of state when one  
wants to simulate dense liquids. I just found it curious that  
Berendsen pressure coupling at 1 atm was not sufficient to quickly  
equilibrate the volume in a system where the vacuum regions are large  
in comparison to the LJ cutoffs.


-- original message --

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 :

[Hide Quoted Text]
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,

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