[gmx-users] Problem with temperature and stochastic dynamics in FEP
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 3 04:55:40 CEST 2011
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
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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