thank you for the rational explanation. but is the free energy change in the charge on/off step(~10kJ/mol) small enough to ignore the flucturations? The free energy change in the LJ mutation step is about 8kJ/mol.
On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub <j...@gwdg.de> wrote: > friendli wrote: > > Dear all, > > > > When I performing mutation free energy calculation from Leu to Ala, I > > first turn off the charge on the side chain of Leu. As I read from the > > GMX archive, the dG/dl curve should be rather smooth for turning off the > > partial charge. > > In this step(charge off/on), however, I can not obtain the expected > > smooth dGdl curve.(see the attachment). I did not use soft-core in this > > step. > > Is this normal because the mutation is relatively large? If not, what > > could be the problem? > > The partial charges of the sidechaines of apolar AA (such as Leu) are > almost zero, that's why your dGdl is almost zero. Only because of the > small dgdl your curve looks non-smooth, but that's just a scale issue here. > > Best, > Jochen > > > > > > > the following is part of the topology file. > > > > 17 opls_238 2 LEU N 7 -0.5 14.0067 ; > > qtot 0.5 > > 18 opls_241 2 LEU H 7 0.3 1.008 ; > > qtot 0.8 > > 19 opls_224B 2 LEU CA 7 0.14 12.011 ; > > qtot 0.94 > > 20 opls_140 2 LEU HA 7 0.06 1.008 ; > > qtot 1 > > 21 opls_136 2 LEU CB 8 -0.12 12.011 > > opls_136 0 12.011 ; qtot 0.88 > > 22 opls_140 2 LEU HB1 8 0.06 1.008 > > opls_140 0 1.008 ; qtot 0.94 > > 23 opls_140 2 LEU HB2 8 0.06 1.008 > > opls_140 0 1.008 ; qtot 1 > > 24 opls_137 2 LEU CG 9 -0.06 12.011 > > opls_137 0 12.011 ; qtot 0.94 > > 25 opls_140 2 LEU HG 9 0.06 1.008 > > opls_140 0 1.008 ; qtot 1 > > 26 opls_135 2 LEU CD1 10 -0.18 12.011 > > opls_135 0 12.011 ; qtot 0.82 > > 27 opls_140 2 LEU HD11 10 0.06 1.008 > > opls_140 0 1.008 ; qtot 0.88 > > 28 opls_140 2 LEU HD12 10 0.06 1.008 > > opls_140 0 1.008 ; qtot 0.94 > > 29 opls_140 2 LEU HD13 10 0.06 1.008 > > opls_140 0 1.008 ; qtot 1 > > 30 opls_135 2 LEU CD2 11 -0.18 12.011 > > opls_135 0 12.011 ; qtot 0.82 > > 31 opls_140 2 LEU HD21 11 0.06 1.008 > > opls_140 0 1.008 ; qtot 0.88 > > 32 opls_140 2 LEU HD22 11 0.06 1.008 > > opls_140 0 1.008 ; qtot 0.94 > > 33 opls_140 2 LEU HD23 11 0.06 1.008 > > opls_140 0 1.008 ; qtot 1 > > 34 opls_235 2 LEU C 12 0.5 12.011 ; > > qtot 1.5 > > 35 opls_236 2 LEU O 12 -0.5 15.9994 ; > > qtot 1 > > > > thank you > > > > Qiang > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > ************************************************ > Dr. Jochen Hub > Max Planck Institute for Biophysical Chemistry > Computational biomolecular dynamics group > Am Fassberg 11 > D-37077 Goettingen, Germany > Email: jhub[at]gwdg.de > Tel.: +49 (0)551 201-2312 > ************************************************ > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
