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
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Received on Mon Sep 12 2016 - 22:30:02 PDT
