[gmx-users] Why Total Energy is positive??

[David Mobley]

> 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 < spoel at xray.bmc.uu.se> 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.
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>