Steven Neumann wrote:
On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
--
========================================
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
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