Subject: Re: [IMP-dev] equilibration in MDOptimizer
From: Friedrich Foerster <>
Date: Fri, 22 Feb 2008 15:04:25 -0800
On Feb 22, 2008, at 2:45 PM, Ben Webb wrote:
Friedrich Foerster wrote:
i discovered the MD optimizer in imp and i am interested in using it.
when studying the input, i am missing something: how is the
temperature equilibrated? there is no parameter for that in the input
(equil in dodgy old modeller). also in the source code i did not
figure out where the temperature is actually used...
is the function safe to be used now? or should i rather not?
MD is currently a very simple implementation, and doesn't do much
beyond
moving the atoms around. You should come talk to me (or hash it out on
the mailing list or wiki) about your specific needs.
i am currently not in the lab and therefore miss the opportunity to
earn a fortune on ebay with old harddisks. do you have an old mac
around? previous lab members dealt pretty antique machines for
significant amounts;)
Equilibration in
particular isn't implemented in the way you might expect, because to
do
it the Modeller Way (temperature and equil arguments to the optimizer)
isn't very general. I instead propose something similar to:
1. An abstract DynamicsAction class from which concrete classes such
as
VelocityScalingThermostat (which is what Modeller's MD does),
NoseHooverThermostat, etc. derive.
sounds good to me. for my purpose, the crude modeller way is probably
sufficient, but more flexibility is certainly good.
2. The MD class maintains a list of DynamicsAction objects and calls
an
evaluate() method on each one at each dynamics step.
Any comments? I don't think using OptimizerStates for this is
appropriate, since they generally are optimizer-agnostic, and probably
shouldn't be tinkering with the optimization state, whereas a
DynamicsAction would be expected to actually go in and mess with the
velocities etc.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle
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