<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">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/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
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