[gmx-users] Problem with temperature and stochastic dynamics in FEP
Sanku M
msanku65 at yahoo.com
Wed Aug 3 17:51:30 CEST 2011
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.
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>
>> *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
>>
>> -- ========================================
>>
>> 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
><mailto:gmx-users at gromacs.org>
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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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