L. Michel Espinoza-Fonseca wrote:
On Sat, Mar 8, 2008 at 11:37 PM, Kristina Woods
<[EMAIL PROTECTED]> wrote:
Hello:
Hello Kristina
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 :)
Yes it is possible. Check mdp options. Read them carefully.
Cheers,
Michel
Thank you,
Kristina
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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