Jason,
sanderAPI tests passed for me. I also compared single point energies on
the dhfr test case. In that case, the energies did match to the 4th
decimal.
My test system is pretty simple: water/ethanol mixture. I'll send you the
files offline in case you want to take a look.
--Niel
On Tue, Sep 13, 2016 at 9:52 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2016 - 10:00:05 PDT
