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 <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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