Hi all. Just informing, I tried a single molecule, and the topology with all dummies minimize (despite taking loads of steps bfgs steps).
The interesting thing is that the distance between atom 6 and 17 at beggining reads 3.1 angstrons, and at the end read 2.9 angstrons. Why it's going bad with many molecules or even single molecule MD, God? Thanks a lot everybody in advance, Sincerally yours, Jones On 10/11/07, Jones de Andrade <[EMAIL PROTECTED]> wrote: > > Hi Prof. David. > > Yes, it a self created topology. This one is based on another self created > topology that runs perfectly for cyclohexane. It was adapted to include the > dummy atoms. > > I guess there is something wrong in the definition of the dummies in the > topology. But I have no clue where it is. Can you provide me some clue on > this? > > I'll run a single molecule now. > > Thanks a lot in advance, > > Sincerally yours, > > Jones > > On 10/11/07, David van der Spoel < [EMAIL PROTECTED]> wrote: > > > > Jones de Andrade wrote: > > > Hi Prof. David. > > > > > > What details do you mean? Actual topology files are attached. Anything > > else? > > > > > > Thanks a lot in advance! > > > > > > Sincerally yours, > > > > > > Jones > > > > > There is something wrong in the topology, youäll have to debug it > > yourself... > > > > -- > > 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 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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