[gmx-users] NPT - umbrella sampling

[Steven Neumann]

On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul <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?

Steven

>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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