[gmx-users] Re: free energy tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jun 6 10:43:28 CEST 2006

Hi David, David et al.

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.

btw. Maybe some are interested to know that the MD introductory course was
also updated (but is still located at



On 6/6/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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