Hi,
pytraj uses sander via its Python interface for energy evaluation.
Can you try to use pysander directly and compare to you sander run (so we
know the source of the difference),
Please see below script:
import parmed as pmd
import sander
# make default pme input
inp = sander.pme_input()
# update to your files
parm_file = '../ubiquitin/prmtop'
rst7_file = '../ubiquitin/restrt.save'
parm = pmd.load_file(parm_file, rst7_file)
with sander.setup(parm_file, parm.coordinates, parm.box, mm_options=inp):
e, f = sander.energy_forces()
print(e.elec)
# gist: https://gist.github.com/hainm/7614bfdd85094b3670de66b687c4f169
cheers
Hai
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*
> vdw_14 = 0.0000
> elec_14 = 1918.5150
> tot = -5386.4819
>
> So this difference is obviously small, but I assumed they would be nearly
> identical. Is it to be expected? I'm using default input parameters for
> both sander and pytraj. I'm guessing there is some part of the PME
> calculation that sander and pytraj do differently?
>
> Thanks for any thoughts on this,
> --Niel
> _______________________________________________
> 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 Mon Sep 12 2016 - 23:00:03 PDT
