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<br><br>> Date: Thu, 5 Feb 2009 10:27:13 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] heat exchanges<br>> <br>> > The integrations errors in the electrostatics have much more effect<br>> > on the water than on the protein, because the water has higher charges<br>> > and is far more mobile. No thermostat can correct for these errors,<br>> > unless you use multiple groups.<br>> <br>> I realize that it is not exactly a "thermostat", but the SD integrator <br>> is expected to correct for these errors using only one temperature <br>> coupling group is it not?<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 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><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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