[gmx-users] Re: free energy tutorial

Tue Jun 6 04:01:21 CEST 2006

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 Mobley
UCSF

On 6/4/06, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Bharat and Matt,
>
>  The tutorial was set up by a colleague of mine, who has left our group a
> while ago. Given your remarks, I think it's better to replace the current
> version with a new one. I hope I can find some time for the revision and
> would welcome any suggestions for changes, additions (topics to cover),
> which can be sent to me off the list. Consider the tutorial in its current
> form deprecated (which I will add as a note in the tutorial soon).
>
>  Best regards,
>
>  Tsjerk
>
> On 6/2/06, mernst at tricity.wsu.edu <mernst at tricity.wsu.edu > wrote:
> > Hi Bharat,
> >
> > This is the same tutorial that led me astray when I first began trying
> free energy
> > calculations in Gromacs. I am not sure how close to the experimental value
> the author
> > intended to get with this hydration free energy tutorial. If you are using
> a recent
> > version of Gromacs, be aware that the soft core method has changed. The
> tutorial says
> > sc-alpha should be 1.51, but that is more appropriate for the older method
> corresponding
> > to sc-power=2 rather than the sc-power=1 that is now recommended.
> >
> > This tutorial also has you simultaneously mutate partial charges and atom
> types. I have
> > recently been informed, and confirmed via observation, that performing the
> partial
> > charge mutation with soft core potentials on can lead to misleading and
> very noisy
> > results. Look in the recent mailing list archives for suggestions and
> papers about
> > splitting the transformation into two series of calculations, one with
> partial charge
> > mutation and no soft core potentials and the other with soft core
> potentials and no
> > partial charge mutation. Even if you don't want to do this for the simple
> tutorial
> > you'll probably want to do it for real systems in the future.
> >
> > Finally, the tutorial gives the dubious advice to use the final structure
> from one
> > window as the starting structure for the next window. If you instead run
> each window's
> > simulations completely independently, you can simultaneously run
> calculations on several
> > machines and don't have to worry about the output of previous windows
> somehow biasing or
> > contaminating the current window. Again, I don't know if it is necessary
> to operate this
> > way to get good results on this simple tutorial, but it does become more
> important if
> > you want to run novel, non-trivial systems in the future.
> >
> > Matt Ernst
> > Washington State University
> >
> > > Dear GMX users,
> > >
> > > i am trying 'relative hydration free energy of p-cresol wrt toluene'
> tutorial
> > > from
> http://md.chem.rug.nl/education/Free-Energy_Course/3.mutation-fe.html
> . i am using
> > > all the mdp files given on
> > > the site, the confout.gro from toluene/eq directory of the previous
> tutorial as starting
> > > structure for this simulation.
> > > and whatever relevant changes has to be made in top and gro have been
> made. then i
> > > performed the simulation for lamda
> > > values from zero to one with an interval of 0.4, so total of 26
> simulations. but i am
> > > not getting the mentioned
> > > experimental value of ddG-hyd.
> > >
> > > i got the following values in rmsd.xvg
> > >
> > >         IN WATER                    IN VACUO
> > > ==========================   ============================
> > > 0    -61.874991   2.59103    0    -98.521845   8.80653
> > > .04  -57.180709   1.73975    .04  -67.562344   0.237903
> > > .08  -58.786951   0.266783   .08  -64.780817   1.23656
> > > .12  -60.764221   0.300319   .12  -63.280561   1.14712
> > > .16  -62.700774    0.313339   .16  -60.123999   0.926409
> > > .20  -65.107642   1.26388    .20  -58.584394   0.103875
> > > .24  -63.749578   0.384702   .24  -56.668703   1.02234
> > > .28  -64.267572   1.22184    .28  -54.837984   0.0807904
> > > .32  -61.524424   0.402878   .32  -53.550764   0.0760657
> > > .36  -55.897929   0.314078   .36  -51.510805   0.0622261
> > > .40  -49.084890   1.05137    .40  -49.736461   0.0627338
> > > .44  -38.339801    1.39297    .44  -48.470839   0.0718284
> > > .48  -29.613058   1.38755    .48  -46.842750   0.0740531
> > > .52  -24.891702   1.04125    .52  -45.007666   0.0766915
> > > .56  -25.435188   1.70549    .56  -43.939682    0.101024
> > > .60  -25.180946   1.82089    .60  -41.844138   0.111544
> > > .64  -28.395296   0.849711   .64  -41.250909   0.13644
> > > .68  -29.672103   2.26016    .68  -41.182423   0.139366
> > > .72  -34.441109    2.00941    .72  -41.747919   0.127424
> > > .76  -39.148106   2.01051    .76  -44.426396   0.143008
> > > .80  -49.360365   2.34239    .80  -44.381975   0.135462
> > > .84  -57.031557   2.79298    .84  -45.564523    0.123685
> > > .88  -64.059494   2.79089    .88  -46.074452   0.104784
> > > .92  -78.668957   1.97957    .92  -46.678656   0.0993529
> > > .96  -85.671014   1.92346    .96  -46.871521   0.0923201
> > > 1.0  -52.956186    1.26136    1.0  -47.183714   0.0934921
> > >
> > >
> > > upon integration in xmgr, following are the dG values:
> > > dG-wat = -50.6556 kJ.mol-1
> > > dG-vac = -51.1109 kJ.mol-1
> > >
> > > ddG-hyd = 0.455 kJ.mol-1
> > >
> > > the experimental value mentioned on the site is -22.1 kJ.mol-1
> > >
> > > Please help...
> > >
> > > bharat
> >
> >
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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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