[gmx-users] A question about quenching
David van der Spoel
spoel at xray.bmc.uu.se
Sun Mar 9 10:12:38 CET 2008
L. Michel Espinoza-Fonseca wrote:
> On Sat, Mar 8, 2008 at 11:37 PM, Kristina Woods
> <kristina.woods at gmail.com> wrote:
> 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.
>> Thank you,
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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