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
