On Tue, Sep 13, 2016 at 6:48 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Sep 13, 2016 at 1:07 AM, Niel Henriksen <shireham.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I'm comparing output for reprocessing a trajectory with sander (ie,
> imin=5)
> > and with pytraj. Everything looks good except for the ELEC values, which
> > differ in the 0.02 - 0.07 range.
> >
> > For example:
> >
> > ### SANDER OUTPUT
> > BOND = 150.8474 ANGLE = 936.1639 DIHED =
> > 153.3573
> > VDWAALS = -319.5965 *EEL = -8225.6990 * HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 1918.5150 RESTRAINT =
> > 0.0000
> > minimization completed, ENE= -.53864119E+04 RMS= 0.149448E+02
> >
> > ### PYTRAJ OUTPUT
> > bond = 150.8474
> > angle = 936.1639
> > dihedral = 153.3573
> > vdw = -319.5964
> > * elec = -8225.7691*
> >
>
>
> Lack of a EGB term and a negative electrostatic term typically means you
> are using PME. If that's the case, imin=5 sets the PME parameters (grid
> size, alpha, etc.) for the first frame and uses that for every subsequent
> frame.
>
>
thanks to Jason's comment about the initial setup, I just have a fix for
pytraj: https://github.com/Amber-MD/pytraj/pull/1303/files
The reason is pytraj used Box info from Topology for sander setup while
pysander use box info from restart file.
Energies from pytraj should be identical to pysander's ones now.
thanks Niel to bring this issue.
cheers
Hai
> If the same PME parameters don't get applied by pysander, then you'll see
> very small differences like this. When I've been careful to make sure this
> kind of discrepancy does not happen, I usually get agreement out to machine
> precision.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Tue Sep 13 2016 - 10:00:03 PDT
