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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 3 18:00:30 CEST 2011


On 4/08/2011 1:51 AM, Sanku M wrote:
> Hi Mark and Justin,
>   I did investigate on the rvdw=rlist issue. But, I found even if I 
> make rvdw < rlist and still keep time step 0.002, the average 
> temperature goes to 303 K.
> Only reducing the time step does help ( even if rvdw=rlist) to get 
> average temperature to 300K.

... and the tau_t issue I mentioned?

Mark

> Sanku
>
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tue, August 2, 2011 11:46:21 PM
> *Subject:* Re: [gmx-users] Problem with temperature and stochastic 
> dynamics in FEP
>
> 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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>>
>
> 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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