<br /><br /><span>On 03/08/11, <b class="name">Sanku M </b> <msanku65@yahoo.com> wrote:</span><blockquote cite="mid:1312339352.86390.YahooMailRC@web114411.mail.gq1.yahoo.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><style type="text/css"><!-- DIV {margin:0px;} --></style><table><tbody><tr><td><p></p><div style="font-family: 'times new roman','new york',times,serif; font-size: 12pt;">
<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></div></td></tr></tbody></table></p></span></div></blockquote><br />Or your use of it... check out manual 7.3.3 and how the value of ref_t is relevant.<br /><br />Mark<br /><br /><blockquote cite="mid:1312339352.86390.YahooMailRC@web114411.mail.gq1.yahoo.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td><div style="font-family: 'times new roman','new york',times,serif; font-size: 12pt;"><div style="font-family: times,serif; font-size: 12pt;"><div ><br/></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 face="Tahoma" size="2"><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 href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br />> *To:* Discussion list for GROMACS users
<<a 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 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" rel="nofollow" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br />> <br />> ========================================<br />> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br />> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="1">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" rel="nofollow" target="1">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 send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br />> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="1">http://www.gromacs.org/Support/Mailing_Lists</a><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" rel="nofollow" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br /><br />========================================<br />-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="1">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" rel="nofollow" target="1">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 send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="1">http://www.gromacs.org/Support/Mailing_Lists</a><br />Blacksburg, VA<br />> jalemkul[at]vt.edu | (540) 231-9080<br /><span>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br />> <br />> ========================================<br />> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br /><span>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="1">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br /><span>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="1">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br />> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
<mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br /><span>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="1">http://www.gromacs.org/Support/Mailing_Lists</a></span><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" rel="nofollow" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br /><br />========================================<br />-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="1">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" rel="nofollow" target="1">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 send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="1">http://www.gromacs.org/Support/Mailing_Lists</a><br /></div></div><div><br/></div>
</div>Blacksburg, VA<br />> jalemkul[at]vt.edu | (540) 231-9080<br /><span>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br />> <br />> ========================================<br />> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br /><span>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="1">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br /><span>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="1">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
posting!</span><br />> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br /><span>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="1">http://www.gromacs.org/Support/Mailing_Lists</a></span><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" rel="nofollow" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br /><br />========================================<br />-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="1">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" rel="nofollow" target="1">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 send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="1">http://www.gromacs.org/Support/Mailing_Lists</a><br />Blacksburg, VA<br />> jalemkul[at]vt.edu | (540) 231-9080<br /><span>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br />> <br />> ========================================<br />> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br /><span>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="1">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br /><span>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="1">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br />> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
<mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br /><span>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="1">http://www.gromacs.org/Support/Mailing_Lists</a></span><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" rel="nofollow" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br /><br />========================================<br />-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="1">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" rel="nofollow" target="1">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 send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="1">http://www.gromacs.org/Support/Mailing_Lists</a><br /><div><br/></div>
<div><br/></div></div></td></tr></tbody></table></p></span></div></blockquote>