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 > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev