Hi
Now, make sure, that you apply the thermodynamic cycle correctly.
I wouldn't wonder about large errors. Depending on the definition of
large. Error estimation from free energy calculations can be very
tricky. Using mpi shouldn't influence your calculations outcome.
Still I don't know the error.
How to post the numbers: Exp. value (+error) and your calculated value
(+error) ? From those I could tell you if something is terribly wrong or
not. :)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
[EMAIL PROTECTED] wrote:
Hi MaiK,
Sorry i forgot the subject. Thank you to have answered this email. This
tutorial is about solvation free energy of toluene using thermodynamical
cycles. two energies have to be calculated according to this cycle, the
hydration energy of toluene and the mutation energy from dummy to toluene
in vacuo. For each energy calculation several MD simulation for different
lambda value must be performed. in the mdp files given i added the line
sc-power=1 and made the calculation. from the file dgdl.xvg obtained for
each lambda value i used the g_analyse command to get the average and the
estimated error of free energy.
i made the plot <dgdl>=f(lambda) for the first part (hydration of toluene)
integrated and get the integrated value of the plot and did the same for
mutation energy of toluene and made the difference of the two integrated
values. I really don't know where the error came from :
-version of gromacs, the fact that mpi has been used for the first part
and single process for the mutation part (because of shake block problem)
won't change anything i guess, I would carefully go through one more time
and check why i didn't get the right value. I don't know if this high
estimated error is really problematic.
regards
geraldine
On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:
Hi
First of all: You can be quite happy, if anyone reads a "no subject"
mail. sc-power seems to be set to zero in the newer version, in contrast
to the old ones, where it was 1 by default. Therefore GROMACS complains. 1
is the value, you should use. I don't know the tutorial, but if you use
exactly the files given there (and add sc-power = 1), you should get
values, which are close to the experimental one (I guess, cause a tutorial
won't make sense, if the files don't yield the desired value).
Sorry, but more help is hard to give with so few information.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
[EMAIL PROTECTED] wrote:
Hi all,
i 'm a beginner in molecular dynamics. I was doing the tutorial of md
group, hydration free energy of toluene :
http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html
i have some problems regarding the calculation of toluene in water. the
thing is that in the examples files equ-10.00.mdp and data-10.00.mdp
no sc-power were mentioned and doing the calculation the error files
mentioned about sc-power must be >0 so i added this line sc-power=1 to
those files. Analyzing the dgdl.xvg files the estimate error(err. est.)
is about 5.79.... for each lambda value studied while the mutation of
toluene to dummy in vacuo gave really reasonable rms of about 10E-5.
Combining the integration value of the plot in water and vacuo did not
give me the right solvation free energy value (compare to experimental
one). i assumed that this is the free calculation in water which is
problematic. I tried to play with sc-power and sc-alpha but still even
if those parameters seem to influence a lot on the energy no real
improvement are visible. Would you have any idea what could be the
problem? geraldine Helsinki university
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