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

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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