> If it is fine, then how can I compare the result with ab inito's? Thanks.
Two things: (1) Total and potential energies are only meaningful up to an additive constant. So there is no reason in principle your potential energy (or total energy) should be negative rather than positive. Just think about gravitational potential energy, for example: If I say that "zero" potential energy is when I have a ball sitting on the ground, then it has a potential energy of m*g*L if I hold it L meters off the ground. But if zero potential energy is at M meters, then it has a potential energy of m*g*(L-M) when I hold it L meters off the ground, and -m*g*M when it's on the ground. (2) You want to compare the total potential energy of your system from an ab initio calculation with that from MD? Why? (That is, what do you hope this will tell you?) (For reason #1, as well as for other reasons, this is not likely to be a meaningful comparison). David > > On 9/5/07, David van der Spoel < [EMAIL PROTECTED]> wrote: > > uki zhu wrote: > > > Hi, gmx-users, > > > These days I am trying to do some systems about carbon tubes. And I > > > found Total Energy of the system is positive whether Energy > > > Minimization or MD. The amount of Total Energy is about E03. > > > > > > For example, > > > "" > > > Step Time Lambda > > > 5000 5.00000 0.00000 > > > > > > Energies (kJ/mol) > > > Morse G96Angle Proper Dih. LJ (SR) Coulomb > (SR) > > > 5.92521e+02 9.76865e+02 6.24199e+03 > -1.72019e+03 0.00000e+00 > > > Potential Kinetic En. Total Energy Temperature Pressure > (bar) > > > > 6.09119e+03 3.32193e+03 9.41312e+03 3.02677e+02 8.29506e-02 > > > "" > > > in a log file. > > > > > > Is anyone who can help me to solve this problem? > > > > > > Thanks very much. > > > > > this is not a problem. it is fine. > > > > -- > > David van der Spoel, Ph.D. > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [email protected] > 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 [email protected] 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
