Hi Chris,
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.
Ciao,
Patrick
Le 23/03/2011 21:06, chris.ne...@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
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.
Chris.
-- 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 .
Ciao,
Patrick
Le 21/03/2011 16:53, chris.ne...@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,
Chris.
--
_______________________________________________________________________
!!!! new E-mail address: patrick.fu...@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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