AMBER Archive (2003)

Subject: AMBER: minimization error

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Thu Aug 14 2003 - 13:23:39 CDT

hi,

I am trying to minimize a protien structure on one of our clusters. the
simulation went fine, but when i checked the min.out file i got weird
values for some of the parameters. below is a part of min.out file

----------------------------------
 NSTEP ENERGY RMS GMAX NAME NUMBER
   1 -nan -nan 2.9855E+15 HB 224

 BOND = 16393.1733 ANGLE = 623.3094 DIHED = 463.8889
 VDWAALS = -nan EEL = -nan HBOND = 0.0000
 1-4 VDW = 497.7016 1-4 EEL = 3080.5624 RESTRAINT = 0.0000

 NSTEP ENERGY RMS GMAX NAME NUMBER
  100 nan nan nan H2 17129

 BOND = nan ANGLE = 179881.8980 DIHED = 0.0000
 VDWAALS = -404.5300 EEL = nan HBOND = 0.0000
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000

 NSTEP ENERGY RMS GMAX NAME NUMBER
  200 nan nan nan H2 17129

 BOND = nan ANGLE = 179881.8980 DIHED = 0.0000
 VDWAALS = -404.5300 EEL = nan HBOND = 0.0000
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000

 NSTEP ENERGY RMS GMAX NAME NUMBER
  300 nan nan nan H2 17129

 BOND = nan ANGLE = 179881.8980 DIHED = 0.0000
 VDWAALS = -404.5300 EEL = nan HBOND = 0.0000
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000
-------------------------------------------------

1. can anyone please explain me why some of the values are "nan". Is there
   a meaning for it in AMBER, if not what might have caused this error.

below is the cluster output file where all errors messages of the
simulation are redirected to.

-------------------------------------------------
***** Processor 7
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 17129 Allocated: 4187
------------------------------------------------

2. can anyone please explain me what the above message means.

Regards
 -Venkat

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