[gmx-users] RDF(PMF) and Umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 17:58:09 CET 2012

Gavin Melaugh wrote:
> Hi Justin
> Just a quick clarification regarding my previous point. With geometry =
> distance, and pull_dim =Y Y Y . Is the pull_group sampling all
> dimensions equally (or without prejudice) about pull_init ?  And iN your

I don't necessarily know if you can say "equally," but all dimensions are 
restrained in some way in response to changes in the COM distance.  I feel like 
this has been discussed before, so there's probably a better answer.

> first reply what did you mean about by "straight pull" ?

A simple one, along a vector, in a direction where the COM distance never 
changes sign (always increasing or always decreasing).  It is the simplest case 
of pulling.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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