I have tried comparing energies and here are the results:
For initial configuration I receive from NAB:
iter Total bad vdW elect nonpolar genBorn
frms
ff: 0 113013.79 4458.86 108611.29 -56.37 0.00 0.00
5.38e+03
and from sander:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.9198E+03 1.7964E+01 7.5305E+01 C90 90
BOND = 193.1278 ANGLE = 3623.6104 DIHED = 642.1252
VDWAALS = 290.9881 EEL = 60.9590 HBOND = 0.0000
1-4 VDW = 226.0755 1-4 EEL = -117.0890 RESTRAINT = 0.0000
and for NAB optimized structure I receive from NAB:
iter Total bad vdW elect nonpolar genBorn
frms
ff: 1 12594.89 9452.47 3194.02 -51.60 0.00 0.00
8.23e-09
Energy = 1.2594885637e+04
RMS gradient = 8.2261245409e-09
and from sander:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 9.5920E+03 1.1470E+02 3.6405E+02 C38 38
BOND = 5177.7234 ANGLE = 3633.9399 DIHED = 640.8082
VDWAALS = 106.1256 EEL = 57.8435 HBOND = 0.0000
1-4 VDW = 84.7384 1-4 EEL = -109.1508 RESTRAINT = 0.0000
And after minimization NAB optimized structure with sander I obtain
again the right (expected) structure. I think that there is something
wrong with my NAB input files or NAB reads bonds from prmtop file
somehow differently than sander.
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Received on Tue Nov 08 2016 - 09:30:02 PST
