Hi all. First, I would like to apologize for the previous message. Maybe I've been too "harsh"? Sorry for that.
Second, I would like to list all the energetic contributions for one (same system, different run) run that g_energy allowed me to get: Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Bond 2.05116 0.0591887 0 -0.123751 - 30.9381 Angle 2.638 0.0664036 0 0.114896 28.7242 LJ (SR) -14.3726 0.0865671 0 -0.0877988 - 21.9499 Disper. corr. -0.378693 0.00211843 0 -0.00185533 - 0.463837 Coulomb (SR) 0.128875 0.0164563 0 0.000956545 0.239138 Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 0.00987542 Coul. recip. -145.145 0.660423 0.652976 -0.00137031 - 0.34258 Potential -10.2211 0.138681 0 -0.0988822 - 24.7207 Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943 0.025986 Total Energy -2.54473 0.167497 0 -0.0987789 - 24.6949 Temperature 123.15 1.5896 1.5896 3.34002e-06 0.000835011 Ok, those are with nmol 500, but it doesn't seem to matter that much. If anybody asks, I can do all them again without that. Any help would be really thankfull! Sincerally yours, Jones On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote: > Hi David! > > Ha, so there is something extra? Thanks a lot.... :) I knew I was > forgeting something. > > So how should I deal with it? I mean, what are the contibutions that are > inside the "Potential" option of g_energy? Does it include all > corrections, disp.corr. ones also, or there is something missing? > these are inside the Coulomb LR (PME) or some other Coulomb term (RF corrections). Energy is of course the sum of all terms. Try without the nmol flag to g_energy first. > Thanks a lot! > > Jones > > On 6/23/07, *David van der Spoel* < [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Jones de Andrade wrote: > > Hi Mark. > > > > Haven't got exactly what you said. So let me rephrase myself: > > > > The CF4 molecule doesn't have dihedrals nor intramolecular LJ and > > coulombic contributions. > > > > What kind of contribution am I missing that makes potential > energy minus > > bond stretching minus angle bending *different* from Lj + > coulomb(SR) + > > coulomb (LR) + Disp correction? > > > > Thanks a lot in advance, > > > > Sincerally yours, > > > > Jones > > > I didn't follow the whole discussion, but there are also exclusion > corrections when using PME or RF. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > <mailto: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] > <mailto:[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 -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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
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