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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Brownina dynamics is a Langevin equation for the coordinates (no inertia).<br>Stochastic dynamics is a Langevin equation for the velocities (with inertia).<br><br>Everything depends on what you want to do, which you do not tell in detail.<br>If you want to leave out the solvent, but you want to simulate a system in solvent,<br>SD is not going to help you, since there is no implicit solvent potential,<br>so your potential and therefore your sampling is nonsense.<br></div><br>tau_t has no effect on the distribution, only on the dynamics.<br>If you want the correct dynamics, you will have fit tau_t to<br>reproduce some kinetic quantity that you are interested in.<br>For different quantities tau_t can be different.<br><br>Berk<br><br><br><hr id="EC_stopSpelling">Date: Thu, 23 Oct 2008 15:31:16 +0200<br>From: omermar@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] stochastic dynamics , langevin<br><br><div dir="ltr">Dear All,<br>I am trying to perform Langevin dynamics of large peptides / proteins.<br>After reading the manual & going over some old mails in this list, I have two points I hope you could clear for me:<br>
[Gromacs version 3.3.3]<br><br>1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics:<br><div style="margin-left: 40px;">integrator = sd ;<br></div><div style="margin-left: 40px;">
bd-fric = 0 ;<br></div><div style="margin-left: 40px;">tau_t = 10 ;<br></div><div style="text-align: left; margin-left: 40px;">ref_t = 300 ;<br></div><div style="text-align: left;">With bd-fric=0, the friction is taken as the inverse tau_t.<br>
<br>2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( <a href="http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html</a> ).<br>
<br>Your help is appreciated. Omer.<br clear="all"></div> <br>Koby Levy research group,<br>Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/" target="_blank">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
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