[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 18 14:57:09 CET 2012

shahid nayeem wrote:
> Dear All
> I am doing umbrella sampling for a protein complex. After analysis I am 
> finding that prifle.xvg has not converged. Now I want to extend 
> simulation. I have already pulled one chain to the length of the box. 
> Can I further pull by extending the box size and add more windows to 
> umbrella sampling. Please suggest.

You would have to use a simple test system to prove that this is a valid 
approach.  Changing the nature of the system for some windows sounds very 
questionable to me, and likely would be to reviewers.

> How one should ascertain the initial box size so that g_wham gives a 
> converged profile.xvg.

You should determine the distance needed to sufficiently separate your 
components, that is, determine the minimum COM distance at which interaction 
between the two species is negligible.  Ideally, they would be non-interacting, 
but with PME, that is not possible.



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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