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

[Justin A. Lemkul]

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

========================================