[gmx-users] toluene tutorial sc-power value
cilpa at users.csc.fi
cilpa at users.csc.fi
Wed Feb 13 18:27:10 CET 2008
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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