Getting "nan" at ELEC energy value

From: jesmin jahan (shraban03_at_gmail.com)
Date: Fri Dec 07 2012 - 22:48:46 CST

Deal NAMD users,

I am trying to get the energy value for protein 1BGX. But I am getting
nan (not a number) in the elec value field. Can anyone tell me how to
solve this problem? Note that, I have used amber files ad Amber was
able to run them successfully.

Thanks in advance.

PARM file in AMBER 7 format
Info: SUMMARY OF PARAMETERS:
Info: 31 BONDS
Info: 40 ANGLES
Info: 38 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 105 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PDB FILE: 3.8147e-06
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 13279 ATOMS
Info: 13422 BONDS
Info: 24368 ANGLES
Info: 46290 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 72899 EXCLUSIONS
Info: 39834 DEGREES OF FREEDOM
Info: 6595 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 6595 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 93388.2 amu
Info: TOTAL CHARGE = -12 e
Info: *****************************
Info:
Info: Entering startup at 0.315991 s, 158.434 MB of memory in use
Info: Startup phase 0 took 0.000143051 s, 158.434 MB of memory in use
Info: Startup phase 1 took 0.0279379 s, 160.652 MB of memory in use
Info: Startup phase 2 took 0.000157118 s, 160.652 MB of memory in use
Info: Startup phase 3 took 8.79765e-05 s, 160.652 MB of memory in use
Info: PATCH GRID IS 4 BY 4 BY 3
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.0769354 0.0134014 -0.057038
Info: LARGEST PATCH (41) HAS 866 ATOMS
Info: Startup phase 4 took 0.0139921 s, 162.781 MB of memory in use
Info: Startup phase 5 took 9.98974e-05 s, 162.781 MB of memory in use
Info: Startup phase 6 took 8.51154e-05 s, 162.781 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.000137806 s, 162.781 MB of memory in use
Info: CREATING 619 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 833 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 7.88861e-31 AT 15.998
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 6.28624e-31 AT 15.998
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 7.44463e-24 AT 15.998
Info: Startup phase 8 took 0.00369811 s, 164.586 MB of memory in use
Info: Startup phase 9 took 0.000102043 s, 164.586 MB of memory in use
Info: Startup phase 10 took 0.000290871 s, 170.855 MB of memory in use
Info: Finished startup at 0.362723 s, 170.855 MB of memory in use

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG

ENERGY: 0 6308.9541 2629.3833 7983.6814
0.0000 nan 114137.1742 0.0000
0.0000 nan nan nan
nan nan nan

Jesmin

--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.

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