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

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 3 04:55:40 CEST 2011

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 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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