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

Sanku M msanku65 at yahoo.com
Wed Aug 3 05:12:11 CEST 2011

Hi Justin,
   I did calculate the average temperature using last 2 ns of the 8ns data. It 
is still same 303K. 

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 
> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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