[gmx-users] Problem with temperature and stochastic dynamics in FEP

[Mark Abraham]

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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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
> >
> > -- ========================================
> >
> > 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
>
> ========================================
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