[gmx-users] position restraint dynamics

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 12 12:46:28 CET 2009

bhargavi ch wrote:
> Hi..dear gromacs users...How do we decide the ideal time to run PR??we 
> are simulating a protein of 260 amino acids  which is a tirmer...we have 
> done the PR for 10 ps first time and 100ps for the second ...i had 
> observed a stable graph in the latter compared with the other...and on 
> what factors does do we decide the time interval in PR

It depends on your ensemble.  If you're using NVT, run PR long enough to see the 
temperature stabilize.  If you're running NPT, run PR until both pressure and 
temperature stabilize.


> lucky.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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