[gmx-users] toluene tutorial sc-power value

[cilpa at users.csc.fi]

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/
>
>
>
> 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. 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/
>>>
>>>
>>>
>>>
>>> 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 :
>>>> 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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