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<div style="font-family:times, serif;font-size:12pt;"><div>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.</div><div>The problem arises when sd integrator is used.</div><div>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 .</div><div><br></div><div>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.</div><div><br></div><div><br></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 8:40:21 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>> So, do you suggest that after minimization, I should generate the velocity at 300K instead ?<br>> i.,e for equilibration,should following the set-up?<br>> <br><br>You should always equilibrate under the desired conditions. Never make sudden changes, or else you're going to damage the stability of the system.<br><br>-Justin<br><br>> gen-vel = yes<br>>> > gen-temp = 300<br>>> > gen-seed = -1<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a rel="nofollow" ymailto="mailto:jalemkul@vt.edu" target="_blank" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users
<<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Tue, August 2, 2011 8:26:16 PM<br>> *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP<br>> <br>> <br>> <br>> Justin A. Lemkul wrote:<br>> ><br>> ><br>> > Sanku M wrote:<br>> >> Hi Justin,<br>> >> I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the following change:<br>> >> gen-vel = yes<br>> >> gen-temp = 280<br>>
>> gen-seed
= -1<br>> >><br>> >> So, essentially, I heated the minimized system up from 280 K with ref_t 300K using sd integrator. But, here also I found the average temperature goes to 303 K( instead of 300 K) .<br>> ><br>> > Unless you did simulated annealing in between, you didn't heat the system, you suddenly jolted the temperature, which is probably not stable. Maybe the integrator/Langevin thermostat does not react well to these conditions. Equilibrate under the conditions you wish to collect data. Your data collection uses NPT, so running NVT at a different temperature and suddenly changing the temperature and introducing pressure coupling is not an appropriate procedure. If nothing else, your data will be unreliable, even if your temperature was correct.<br>> ><br>> <br>> Sorry, misread the previous .mdp settings. You're still using
NVT, but the point about the temperature is still valid here.<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 rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a
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