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

[David]

On Tue, 2005-10-25 at 09:21 -0700, David Mobley wrote:
> 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.

OK, can you please submit a bugzilla and attach 2 tpr files, one with
the original coords/velocities and one with other ones, and a trr file
containing max 5 frames?


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