Sanku M wrote:
OKK, But, before, I have tried using md as integrator where I start the
initial velocity as 280K ( which makes sense as the minimized
configuration is essentially at low temperature) and have used
Nose-hoover at 300K and I never had problem in getting the desired 300K
after running a short NVT simulation as equilabration.
The problem arises when sd integrator is used.
In fact, I just tried to generate the initial velocity at 300K along
with sd integrator. I got the 303 K as average temperature again. The
same simulation using md integrator always gives rise to 300K as average
temperature( when used in conjunction with Nose-Hoover ) , even if I
generate velocity at 280 K or 300K .
I guess that the initial velocity-generation temperature should not be
an issue here. The sd integrator in contrast to md integrator may be the
problem.
I have never had such a problem when using sd. I can always achieve the target
temperature within 0.5 K, if not exactly, so I do not believe there is an
inherent problem with sd. Your first post indicated that your statistics were
collected over the entire timeframe, which will not be correct for reasons I
have already described. The initial frames will represent unequilibrated data
that may skew the averages. What if you analyze only the last half of the time?
The last 1 ns?
-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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