[gmx-users] toluene tutorial sc-power value

Fri Feb 15 10:07:46 CET 2008

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/

cilpa at users.csc.fi 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/
>>
>>
>>
>> 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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