[gmx-users] NPT - umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 13:00:26 CET 2012

Steven Neumann wrote:
> Dear Justin and Gmx Users,
> I extracted 42 frames from my trajctory of pulling ligand away from my 
> protein (no position restarined). I would like to run NPT before running 
> umbrella sampling simulations. As far I see Justin in his tutorial NPT 
> and umbrella sampling mdp files looks the same which means you did not 
> restrain whole protein in your system during NPT? Why?

The system at hand was very robust and as such, complete restraints were not 
necessary.  Please do not adhere strictly to the umbrella sampling tutorial; 
there are elements of it that may not be generally applicable (and I'm fairly 
sure there are warnings of this in the tutorial).  It is a simple example 
designed to provide the conceptual and practical basis for such simulations.

> Shall rund NPT withou restraining protein and ligand before umbrella 
> sampling in each window?

Do what makes sense in your case.  Typically, position restraints are applied 
during equilibration.



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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