[gmx-users] Re: free energy tutorial
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 6 08:56:04 CEST 2006
David Mobley wrote:
> Bharat, Matt, Tsjerk, and all,
> I just put a bit of a tutorial on free energy calculations up at
> 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).
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 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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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