On 3/08/2011 2:23 PM, Sanku M wrote:
Finally, I achieved the desired 300K average temperature using sd
integrator . I had to reduce the time step from 0.002 ps to 0.001 ps
and then running the NVT could produce 300K as average temperature.
Still Not sure why md integrator still could 300K average temperature
using 0.002 ps as time-step.
So your integration step was too large to conserve energy. There have
been two suggestions made about why that might be true. Have you
investigated them?
Mark
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Tue, August 2, 2011 10:16:17 PM
*Subject:* Re: [gmx-users] Problem with temperature and stochastic
dynamics in FEP
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 <mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto: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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> 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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