<br><br><div><span class="gmail_quote">On 7/31/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br><br>Date: Mon, 31 Jul 2006 07:21:46 -0700
<br>From: "David Mobley" <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>><br>Subject: Re: [gmx-users] langevin dynamics<br><br>Gerrit is right, with "sd", the friction is set by tau_t, as described
<br>in the section on SD in the manual. In my hands, different tau_t with<br>sd does make a significant difference in what goes on...<br><br>David<br><br><br>On 7/31/06, Gerrit Groenhof (RUG) <<a href="mailto:g.groenhof@rug.nl">
g.groenhof@rug.nl</a>> wrote:<br>> I think you do not use the bd_fric in combination with sd, but with bd,<br>> the friction is set by the tau_t instead. Did you als use different<br>> parameters for that?<br>
><br>> For bd, you would use the friction bd_fric to set the ld friction, but<br>> not for sd, but I could be wrong here...<br></blockquote></div><br>I know this is correctly mentioned in the manual, but if you look at the
mdout.mdp file, it says:<br><br>; LANGEVIN DYNAMICS OPTIONS<br>; Friction coefficient (amu/ps) and random seed<br>bd-fric = 0<br>ld-seed = 1993<br><br>which just makes things more confusing than they already are. Maybe a suggestion to more clearly indicate the bd and sd parameters in there?
<br><br>-- <br>greetings, Pim