David Mobley wrote:
Bharat, Matt, Tsjerk, and all,
I just put a bit of a tutorial on free energy calculations up at
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial.
This will probably be a work in progress; it is not as step-by-step as
Tsjerk's (although possibly I could make it that way later), but it IS
current for GROMACS 3.3/3.3.1. Feel free to contact me directly if
there are any comments/questions/problems.
I should mention at this point the tutorial just covers disappearing
neutral methane in water; I'll probably expand it later. I do think
this should probably be a standard test case for people starting off
on free energy calculations, as Michael Shirts and I have both
calculated values for this in GROMACS with OPLS-AA (and our results
agree quite well, always a plus).
Thanks David,
I've now put up a list of on-line tutorials under Documentation/Tutorial
on the website. Please let me know if there are other resources that
could be added.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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