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salilab / pmi

Python Modeling Interface
https://integrativemodeling.org/nightly/doc/ref/namespaceIMP_1_1pmi.html
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Why is SerialMover used? #229

Closed sethaxen closed 7 years ago

sethaxen commented 7 years ago

Perhaps I'm wrong, but it looks like IMP.core.SerialMover is used in IMP.pmi.samplers.MonteCarlo to propose movers in order, one for each Monte Carlo step. My understanding is that this mover is only recommended when using an incremental scoring function.

Pellarin commented 7 years ago

SerialMover enables a Gibbs Sampling scheme, where particles (ie, XYZ, RigidBodies, Scales) are all moved once. Nowhere is strictly recommending this mover with incremental scoring function, or at least I don't quite understand your question.

shruthivis commented 7 years ago

Agree with Riccardo, given a list of movers (eg. individual bead movers,rigid body movers..) it enables performing an MC step once per mover in the order specified in the list (Gibbs sampling essentially). The SerialMover only specifies how the Gibbs sampling is done and doesn't impose any requirements on the scoring function.

On Fri, Mar 17, 2017 at 3:50 AM, Riccardo Pellarin <notifications@github.com

wrote:

SerialMover enables a Gibbs Sampling scheme, where particles (ie, XYZ, RigidBodies, Scales) are all moved once. Nowhere is strictly recommending this mover with incremental scoring function, or at least I don't quite understand your question.

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Pellarin commented 7 years ago

Should we close this?

sethaxen commented 7 years ago

Yes, thanks, you guys are absolutely right.