[gmx-users] Simulations in extreme conditions
C.Pruteanu at ed.ac.uk
Sat Feb 15 22:48:14 CET 2014
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.
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
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
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.
Centre for Science at Extreme Conditions
University of Edinburgh, UK
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