[gmx-users] toluene tutorial sc-power value
mgoette at mpi-bpc.mpg.de
Thu Feb 14 09:57:16 CET 2008
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
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
cilpa at users.csc.fi 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.
> On Wed, February 13, 2008 6:19 pm, Maik Goette wrote:
>> 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.
>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> 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/
>> cilpa at users.csc.fi wrote:
>>> Hi all,
>>> i 'm a beginner in molecular dynamics. I was doing the tutorial of md
>>> group, hydration free energy of toluene :
>>> 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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