[gmx-users] toluene tutorial sc-power value

cilpa at users.csc.fi cilpa at users.csc.fi
Fri Feb 15 15:08:53 CET 2008 

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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