[gmx-users] toluene tutorial sc-power value

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Feb 15 15:37:22 CET 2008 

Fine :)
So forget what I wrote before...I mentioned exactly that :)

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
> I made the calculation with sc-power=2 adding 3 lambda values. Now i get
> integrating the plot of average free energy for the mutation of toluene in
> water 0.559 instead of 15,8 in previous calculation.
> if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1
> KJ/mol exp.). This is quite ok!!!!!! :)
> So the error was a combination of number of points- sc-parameter but for
> sure number of points are really important for the integration part!!! in
> the calculation of free energy.
> . regards
> geraldine
> 
> 
> On Fri, February 15, 2008 11:07 am, Maik Goette wrote:
>> 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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