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 <[EMAIL PROTECTED]> 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, [EMAIL PROTECTED] <[EMAIL PROTECTED] > 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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