I had a veeery short look into the tutorial and found an error.
DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong.
The correct cycle would be:
DG_1+DG_3=DG_hyd+DG_2
=>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0
So its:
DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3
Anyway, this won't help you, cause the only effect is a change of the
sign to +19 and therefore worse.
Can you show me the topology, you made?
As far as the free energy experts here discussed it, sc-power=2
shouldn't be the lambda-dependance of choice.
I can agree to that from my simulations.
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
the energy
DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water)
for fisrt one deltaG_mutation(vacuo) =-2,85
for second deltaGmutation(water) =15,87
so i found DEltaG_hyd = -19 kj/mol
instead of -3,1 kj/mol
i'll do a series of calculation with sc-power=2 and see the difference
see if there's some significant difference.
geraldine
On Thu, February 14, 2008 10:57 am, Maik Goette wrote:
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.h
tml
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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