[gmx-users] Umbrella sampling's equilibration runs

[Justin Lemkul]

On 5/3/13 2:21 PM, James Starlight wrote:
> Couple extra question about umbrella
>
> Does it possible to use Collective variable (eigenvector from EDA or NMA)
> as the pulling coordinate?
> Does it possible to use output from essential dynamics sampling (here I can
> use EDS in targeted mode to pull my structure to the target conformation)
> for the umbrella's NPT+MD. What the input data in the mdp files must be in
> that case using CV?
>

The restraints implemented within the pull code are simply harmonic potentials 
or rigid constraints along physical vectors.  If you want more abstract versions 
of umbrella sampling, that sounds like a task for something like PLUMED.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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