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Hi,<br><br>With SD there are no temperature differences to be expected when the total<br>temperature is correct.<br>It could only go wrong in the very rare case that one group heats due to cut-off<br>effects and another one cools due to inaccurate constraints.<br>But because you get the same temperature at both tau_t's you can be certain<br>there are no problems.<br><br>The energy fluctuation issue is strange, I thought this was all fixed by now.<br>But maybe you use a strange continuation procedure.<br><br>Berk<br><br>> Date: Thu, 5 Feb 2009 15:08:26 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] heat exchanges<br>> <br>> Thank you Berk,<br>> <br>> I have checked my temperature and find that there is no difference while <br>> using tau_t=0.1 or 1.0 (~2 ns):<br>> tau_t=0.1: temp=303.36 +/- 1.90<br>> tau_t=1.0: temp=303.31 +/- 1.98<br>> <br>> While using only one temperature coupling group, how would I ensure that <br>> the temperature of water is<br>> the same as that of DPC?<br>> <br>> I do see the large depression of diffusion that is induced by tau_t=0.1 <br>> and is pointed out in your thesis:<br>> <br>> Diffusion of tip4p:<br>> tau_t=0.1: 1.43 +/- 0.003<br>> tau_t=1.0: 2.81 +/- 0.136<br>> md with berendsen = 3.115 +/- 0.056<br>> <br>> Diffusion of DPC detergent:<br>> tau_t=0.1: 0.0323 +/- 0.003<br>> tau_t=1.0: 0.137 +/- 0.02<br>> md with berendsen = 0.0928 +/- 0.045<br>> <br>> PS: Note that the RMSD values for the temperature above are from my own <br>> calculation as those from g_energy<br>> in gmx 3.3.1 and 4.0.3 are nonsensical to me :<br>> <br>> Energy Average RMSD Fluct. Drift <br>> Tot-Drift<br>> -------------------------------------------------------------------------------<br>> Temperature 303.3 474.854 474.854 -3.75465e-05 <br>> -0.0976211<br>> <br>> probably because thie .edr was generated by eneconv on all my 200 ps <br>> segments.<br>> Indeed, g_energy on a single segment gives me a sensible RMSD value.<br>> <br>> Thanks again,<br>> Chris.<br>> <br>> #####################<br>> -- original message --<br>> <br>> Yes, the SD "thermostat" has the huge advantage that it thermalizes each<br>> degree of freedom separately.Therefore you never have incorrect temperature<br>> distributions in your system, unless you have very serious integration<br>> artifacts. SD also avoid any ergodicity problems.<br>> <br>> BTW You should check your temperature for your SD runs with tau_t=1.<br>> I often use 1, but that is with a shifted LJ potential and not with a <br>> twin-range<br>> setup that introduces some errors. You might need to change to tau_t=0.5.<br>> tau_t=1 has nearly no effect on the dynamics of water, whereas tau_t=0.5<br>> slows it down somewhat. See chapter 2 of my thesis for numbers for SPC<br>> (which diffuses twice as fast as real water):<br>> http://dissertations.ub.rug.nl/faculties/science/2002/b.hess/<br>> <br>> Berk<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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