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.
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 - 04:00:03 PDT
