[gmx-users] Problem with temperature and stochastic dynamics in FEP
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 3 05:16:17 CEST 2011
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.
> *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 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 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
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users