Sanku M wrote:
Hi Justin,
I did calculate the average temperature using last 2 ns of the 8ns
data. It is still same 303K.
Going back to the original .mdp file, I can see that you're using some incorrect
settings. You've set rlist=rvdw even though you're using a shifted potential
for van der Waals interactions. Surely grompp should have warned you that this
would lead to poor energy conservation. Your solvent is probably heating up as
a result and leading to the incorrect temperature.
-Justin
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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 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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--
========================================
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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