<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"> 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.</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt">Still Not sure why md integrator still could 300K average temperature using 0.002 ps as time-step.</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span
style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, August 2, 2011 10:16:17 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP<br></font><br>
<br><br>Sanku M wrote:<br>> Hi Justin,<br>> I did calculate the average temperature using last 2 ns of the 8ns data. It is still same 303K. <br>> <br><br>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.<br><br>-Justin<br><br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Tue,
August 2, 2011 9:55:40 PM<br>> *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP<br>> <br>> <br>> <br>> Sanku M wrote:<br>> > 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.<br>> > The problem arises when sd integrator is used.<br>> > 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 .<br>> ><br>> > 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.<br>> ><br>> ><br>> <br>> 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?<br>> <br>> -Justin<br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia
Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or
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