[gmx-users] Umbrella sampling's equilibration runs

Justin Lemkul jalemkul at vt.edu
Fri May 3 21:07:08 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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