[gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water
patrick.fuchs at univ-paris-diderot.fr
Thu Mar 24 09:56:39 CET 2011
I fully agree with your analysis about the effect of non-bonded
interactions that accelerate the collapse when the layer of vacuum
around the system is thin. I also observed that it is way faster to
reach equilibrium density in this case.
Le 23/03/2011 21:06, chris.neale at utoronto.ca a écrit :
> 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
> 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,
!!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
Dynamique des Structures et Interactions des Macromolécules Biologiques
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