[gmx-users] Problem with temperature and stochastic dynamics in FEP
msanku65 at yahoo.com
Wed Aug 3 05:12:11 CEST 2011
I did calculate the average temperature using last 2 ns of the 8ns data. It
is still same 303K.
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, August 2, 2011 9:55:40 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
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
> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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