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

[David Mobley]

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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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