hi concerning the cycle i saw this error since i started the tutorial, i paid attention to that but as you said it's not that important since my energy value is too high. i'm right now doing the problem again with sc-power=2 and also 10 points is it enough to have an approximate correct value since i have to integrate the average energy plot by xmgrace, i don't know what kind of integration they use, trapezoid? or... it could have an effect if i don't have enough point. but then .. here attached is my top. file. 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/ > > > > [EMAIL PROTECTED] 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/ >>> >>> >>> >>> >>> [EMAIL PROTECTED] 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/ >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> [EMAIL PROTECTED] 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 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>>> Please search the archive at http://www.gromacs.org/search >>>>>> before posting! Please don't post (un)subscribe requests to the >>>>>> list. Use the www interface or send it to >>>>>> [EMAIL PROTECTED] Can't post? Read >>>>>> http://www.gromacs.org/mailing_lists/users.php >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> . >>>>>> >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! Please don't post (un)subscribe requests to the list. Use >>>>> the www interface or send it to [EMAIL PROTECTED] >>>>> Can't >>>>> post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! Please don't post (un)subscribe requests to the list. Use >>>> the www interface or send it to [EMAIL PROTECTED] Can't >>>> post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>>> >>>> . >>>> >>>> >>>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] Can't >>> post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] Can't post? >> Read http://www.gromacs.org/mailing_lists/users.php >> >> >> . >> >> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >
toluene.top
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