[gmx-users] Simulations in extreme conditions
Dr. Vitaly Chaban
vvchaban at gmail.com
Sat Feb 15 23:52:45 CET 2014
On Sat, Feb 15, 2014 at 10:47 PM, CipPruteanu <C.Pruteanu at ed.ac.uk> wrote:
> Dr. Vitaly Chaban wrote
>> I like extreme conditions... Seriously.
>> OPLS water, as well as other popular MM waters, are parametrized for
>> liquid state. I think you need to decrease model's dipole moment and
>> you have to work with an integration time-step to ensure adequate
>> energy conservation at ca. 600K.
>> I believe there should be exotic water models that were trained to
>> reproduce the phase diagram to certain extent.
> Dear Vitaly,
> I am aware of the fact that GROMACS "doesn't really like" crystal structure,
> but this is generally fine with me since I run my simulations in a region
> which is experimentally know to be liquid state (both the water and
> methane). I am aware t hat it works best with liquids, and that is very well
> since it is exactly the liquid phases of the mixture that I'm interested
At 600K and under 25kbar ... water&methane mixture ... liquid state
.... Hmmmm. Did you point out incorrect pressure?
> The energy conservation looks fine throughout the whole 10 ns of most of my
> simulations, however I'm not quite sure about how to decrease the dipole
> moment of the model (or where exactly to do this, i.e. in which file). If
> you can provide any suggestions on how to do this I would be more than
It is not that easy. You should first compute water's dipole moment
for the simulated conditions.
> The same applies for the more exotic water models. Unfortunately most people
> around me using GROMACS work on biological systems, and I'm the only black
> sheep trying to use it under extreme conditions. I will look for water
> models trained for extreme conditions, but from my initial overview of the
> literature there hardly seemed to be any.
Something should exist. I hear such statements from different people
from time to time.
Dr. Vitaly V. Chaban
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