Re: Getting "nan" at ELEC energy value

From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Dec 08 2012 - 00:22:13 CST

sounds like something is wrong with your parameters, or your coordinates.
NaN often indicates a value that is too high to record, and so usually
happens when your simulation coordinates are far from reasonable.

On Fri, Dec 7, 2012 at 11:48 PM, jesmin jahan <shraban03_at_gmail.com> wrote:

> 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.
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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