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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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