<br><br><div><span class="gmail_quote">2008/1/9, Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br><br><br>________________________________<br>> Date: Wed, 9 Jan 2008 15:30:38 +0200<br>> From: <a href="mailto:beavered@gmail.com">beavered@gmail.com</a><br>> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>> Subject: [gmx-users] Re: Targeted MD<br>><br>><br>> Ran Friedman wrote:<br>>>Dear Stanislav,<br>>><br>>>AFAIK there's no "targeted MD" in GMX. You can run EDS or use the
<br>>>flooding algorithm.<br>>><br>>>Ran.<br>><br>> Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do targeted MD" in GMX.<br><br>Did you add position restraint to your protein
<br>topology?</blockquote><div><br>No, I did not. <br>What group must be restrained therefore? Whole protein or whole protein except loop?<br></div></div><br>