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
--
========================================
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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