[gmx-users] (no subject)
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 23 13:17:43 CEST 2004
On Thu, 2004-09-23 at 12:57, Robert d'Rozario wrote:
> Cheers for the responses, I should have told you all that I have computed
> the rmsd of my molecule, checked the temperature. The rmsd completely
> levels off very suddenly. Any other suggestions?
Not rmsd, but msd. (g_msd)
It could freeze in reality as well. Do you have separate temperature
coupling for solvent and solute?
>
> On Thu, 23 Sep 2004, David van der Spoel wrote:
>
> > On Thu, 2004-09-23 at 11:53, Robert d'Rozario wrote:
> > > Hi,
> > >
> > > I was wondering if anyone has this same problem, its a bit worrying.
> > > I am simualting an alpha helix in DMSO with PME. I have 3 separate
> > > trajectories, each a continuation. The first one runs from 0-4ns then
> > > 2nd one 4-6ns then the 3rd 6-10ns. I have then concatenated the files
> > > which runs from 0-10ns. At 6.1 ns I viewed the system, using VMD, and it
> > > seems to freeze as if the positon restraints are on everything.
> > >
> > > Any help would be greatfully appreciated
> > start by checking energy terms, temperature,pressure. Then compute a
> > mean square displacement for your molecule.
> > >
> > > Robert D'Rozario
> > >
> > > _______________________________________________
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> > --
> > 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
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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> >
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--
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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