[gmx-users] mdrun -rerun results depend on starting .gro file. Why?

[David Mobley]

Dear David and all,

Please see this earlier thread from Michael Shirts:
http://www.gromacs.org/pipermail/gmx-users/2003-December/008429.html. I
think the problem we're seeing is the same one he reported there. It's
possible there are other issues as well, as in our case we're not using
pressure regulation so the box size shouldn't be changing.

Thanks,
David

On 10/25/05, David Mobley <dmobley at gmail.com> wrote:
>
> Dear David,
>
> The specific energies which are different are:
> LJ (SR)
> Coulomb (SR)
> Coulomb recip.
> Potential
> Total energy
> dVpot/dlambda
> Pressure
>
> Again, I can make these nearly match the previous run if I use the correct
> .gro file -- but the results I get for these are CLEARLY dependent on the
> .gro file used, even though I am using the full precision trr files
> including velocities.
>
> Thanks,
> David
>
>
> On 10/25/05, David <spoel at xray.bmc.uu.se> wrote:
> >
> > On Tue, 2005-10-25 at 06:33 -0700, David Mobley wrote:
> > >
> >
> > >
> > > David,
> > >
> > > I'm rerunning with a trr file containing velocities. And the potential
> > > energies are different, as are total energies, etc. Additionally, the
> > > calculations I'm looking at at the moment are free energy
> > > calculations, so the dv/dlambda values are different as well.
> >
> > I don't think the rerun option has ever been tested with free energy, if
> > it works your statistics will be far inferior from the original.
> >
> > But please be more specific. Which energy terms are different?
> >
> >
> > --
> > 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<http://xray.bmc.uu.se/%7Espoel>
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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