[gmx-users] NPT - umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 13:15:11 CET 2012

Steven Neumann wrote:
> On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>     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
> Maybe I asked my qestion not directly. Why during the equilibration of 
> your system (tutorial) NPT before umbrella sampling in each window you 
> restarined only Chain B like in further umbrella samplin (your mdp files 
> of NPT and MD are the same) instead of restraining all chains as it 
> should be during the equilibration?

What "should be" depends on the system.  In my case, the structures were 
extremely robust and did not require full restraints to achieve adequate 
equilibration.  This is not generally true and full restraints are normally applied.



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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