[gmx-users] Problem with temperature and stochastic dynamics in FEP
Mark Abraham
mark.abraham at anu.edu.au
Wed Aug 3 05:07:35 CEST 2011
On 03/08/11, Sanku M <msanku65 at yahoo.com> wrote:
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> 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 .
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> 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.
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Or your use of it... check out manual 7.3.3 and how the value of ref_t is relevant.
Mark
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> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tue, August 2, 2011 8:40:21 PM
> Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
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> Sanku M wrote:
> > Hi Justin,
> > So, do you suggest that after minimization, I should generate the velocity at 300K instead ?
> > i.,e for equilibration,should following the set-up?
> >
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> You should always equilibrate under the desired conditions. Never make sudden changes, or else you're going to damage the stability of the system.
>
> -Justin
>
> > gen-vel = yes
> >> > gen-temp = 300
> >> > gen-seed = -1
> >
> > ------------------------------------------------------------------------
> > *From:* Justin A. Lemkul <jalemkul at vt.edu>
> > *To:* Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> > *Sent:* Tue, August 2, 2011 8:26:16 PM
> > *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP
> >
> >
> >
> > Justin A. Lemkul wrote:
> > >
> > >
> > > Sanku M wrote:
> > >> Hi Justin,
> > >> I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the following change:
> > >> gen-vel = yes
> > >> gen-temp = 280
> >
> >> gen-seed
> = -1
> > >>
> > >> So, essentially, I heated the minimized system up from 280 K with ref_t 300K using sd integrator. But, here also I found the average temperature goes to 303 K( instead of 300 K) .
> > >
> > > Unless you did simulated annealing in between, you didn't heat the system, you suddenly jolted the temperature, which is probably not stable. Maybe the integrator/Langevin thermostat does not react well to these conditions. Equilibrate under the conditions you wish to collect data. Your data collection uses NPT, so running NVT at a different temperature and suddenly changing the temperature and introducing pressure coupling is not an appropriate procedure. If nothing else, your data will be unreliable, even if your temperature was correct.
> > >
> >
> > Sorry, misread the previous .mdp settings. You're still using
> NVT, but the point about the temperature is still valid here.
> >
> > -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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> 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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> 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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.
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> Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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