Sai Pooja wrote:
<snip>
Do you run any equilibration prior to applying these parameters?
Both N-H and P-R allow for wide fluctuations in temperature and
pressure, respectively, which are exacerbated by systems that are
not sufficiently equilibrated. Hence it could take a very long time
if you do not equilibrate well using, i.e. a weak coupling scheme first.
I usually start with a pressure nearby. For example, I start with a
system which was equilibrated at p=71 and then run npt at p=69. Is that
not sufficient?
How do you determine the pressure before the simulation has begun? Moreover,
freezing your system in one dimension can certainly complicate matters, since
that is a non-equilibrium restraint on the dynamics. That could be a factor.
-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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