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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Fri, 3 Oct 2008 22:26:29 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Heat Flux and Lambda<br>> <br>> Andy Shelley wrote:<br>> > David,<br>> > <br>> > I looked up the euqation for the Nose-Hoover thermostat and don't <br>> > understand where lambda comes from and how to use the number of <br>> > degreees of freedom to determine the heat flux of a group. Could you <br>> > explain some more?<br>> Aha, this only works for Berendsen I would think.<br><br>The same equation might not work, but one can do something similar.<br><br>The velocities are scaled each step by lambda, which you can get with g_energy.<br>The heat flux per degree of freedom is therefore simply: 0.5*k_B*T*(lambda^2 - 1).<br>The number of degrees of freedom for temperature coupling groups is printed<br>somewhere at the beginning of the log file.<br><br>Berk<br><br>> > <br>> > Thanks,<br>> > Andy<br>> > <br>> > > I have been reading through the mailing list and have read some<br>> > > discussion that heat flux can be indicated by the value of lambda. Can I<br>> > > calculate the amount of heat flux from the lambda value?<br>> > In principle yes. Look up the equation for the temperature coupling. You<br>> > will need to know the number of degrees of freedom as printed in md.log<br>> > file.<br>> > ><br>> > > Thanks,<br>> > > Andy Shelley<br>> > ><br>> > ><br>> > > ------------------------------<br>> > ------------------------------------------<br>> > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org <br>> > <mailto: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 <br>> > 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>> > <mailto:gmx-users-request@gromacs.org>.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > --<br>> > David.<br>> > ________________________________________________________________________<br>> > David van der Spoel, PhD, Professor of Biology<br>> > Dept. of Cell and Molecular Biology, Uppsala University.<br>> > Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> > phone: 46 18 471 4205 fax: 46 18 511 755<br>> > spoel@xray.bmc.uu.se <mailto:spoel@xray.bmc.uu.se> spoel@gromacs.org <br>> > <mailto:spoel@gromacs.org> http://folding.bmc.uu.se <br>> > <http://folding.bmc.uu.se/><br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> > <br>> > <br>> > ------------------------------------------------------------------------<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>> <br>> -- <br>> David.<br>> ________________________________________________________________________<br>> David van der Spoel, PhD, Professor of Biology<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<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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