[gmx-users] Re: free energy tutorial

Sun Jun 4 13:45:27 CEST 2006

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
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

-- 

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060604/046bffd8/attachment.html>