On Tue, Sep 13, 2016 at 12:48 PM, Niel Henriksen <shireham.gmail.com> wrote:
> Thanks Hai,
>
> Earlier, I tested this by changing ntc/ntf to 2 in pysander and didn't see
> any change, so I assumed it was not the culprit. I guess I should have
> also tried it with sander.
>
> But it raises another issue: why don't the pysander results change when I
> set it's ntc/ntf to 2?
>
>
I did the same thing (set ntc and ntf for pysander) and asked myself too.
We'll wait for Jason's comment.
Hai
> Thanks,
> --Niel
>
> On Tue, Sep 13, 2016 at 9:41 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > 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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> > >
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Received on Tue Sep 13 2016 - 10:00:04 PDT
