Hi David, David et al.<br><br>Thanks for the comments and suggestions so far. Given that David (M) now has a functional Free Energy tutorial online, I've added a note to the current page that it won't work with newer versions of Gromacs and added a link to Davids tutorial. Full revision of the page will be done later.
<br><br>btw. Maybe some are interested to know that the MD introductory course was also updated (but is still located at <a href="http://md.chem.rug.nl/education/mdcourse/">http://md.chem.rug.nl/education/mdcourse/</a>).<br>
<br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 6/6/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
David Mobley wrote:<br>> Bharat, Matt, Tsjerk, and all,<br>><br>> I just put a bit of a tutorial on free energy calculations up at<br>> <a href="http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial">
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial</a>.<br>><br>> This will probably be a work in progress; it is not as step-by-step as<br>> Tsjerk's (although possibly I could make it that way later), but it IS
<br>> current for GROMACS 3.3/3.3.1. Feel free to contact me directly if<br>> there are any comments/questions/problems.<br>><br>> I should mention at this point the tutorial just covers disappearing<br>> neutral methane in water; I'll probably expand it later. I do think
<br>> this should probably be a standard test case for people starting off<br>> on free energy calculations, as Michael Shirts and I have both<br>> calculated values for this in GROMACS with OPLS-AA (and our results
<br>> agree quite well, always a plus).<br>><br>Thanks David,<br><br>I've now put up a list of on-line tutorials under Documentation/Tutorial<br>on the website. Please let me know if there are other resources that<br>
could be added.<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>