[gmx-users] A question about quenching
L. Michel Espinoza-Fonseca
mef at ddt.biochem.umn.edu
Sun Mar 9 06:49:45 CET 2008
On Sat, Mar 8, 2008 at 11:37 PM, Kristina Woods
<kristina.woods at gmail.com> wrote:
> I am interested in running simulations on (binary) mixtures of n-alkanes
> with the hope of learning something more about phase separation in the
> mixtures. One of the things that I would like to do is to try to somewhat
> mimic the experiments that we do in the lab by initially keeping the system
> at a temperature above the melting point of the two different n-alkanes and
> then rapidly cooling the system in a single step (quenching) to place the
> system in an unstable state. Does anyone happen to know how or if it is
> possible to set up such a simulation? Particularly the rapid cooling part?
> I would be curious to hear any comments or advice for setting up and
> carrying out such a simulation.
I think the best approach here will be to use a "modified" simulated
annealing. I said "modified" because usually you'd like the cooling
stage of the annealing to be as slow as possible (similar as when you
grow a crystal); so in your case you could perform a simulation of
your system by heating it up to a target temperature and then by using
a few steps of simulated annealing cool it down.
I'm not sure about how to perform simulated annealing in gromacs,
though. I guess we'll wait for the input of other users here :)
> Thank you,
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