errors in energy minimization

From: Wei Liu (wei.liu_at_biosci.ki.se)
Date: Tue Apr 24 2007 - 05:27:52 CDT

Dear all,

I am a new user of namd as well as MD simulation. I solvated a protein-DNA complex with a water-box and defined the periodic boundary conditions in the configuration file. The box defined by cellBasisVectors has the dimensions 147, 138, 79 and the PME grid dimensions of 120, 120, 60. At the beginning of energy minimization, the following information was output.

TCL: Minimizing for 100 steps

PRESSURE: 0 nan nan nan nan nan nan nan nan nan

GPRESSURE: 0 nan nan nan nan nan nan nan nan nan

ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY

MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPR

ESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 43597.4233 99999999.9999 7143.9524 16.9429 -456282.7726 99999999.9999 0.0000

0.0000 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000 99999999.9999 9999999

9.9999 1602594.0000 99999999.9999 99999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE

INITIAL STEP: 1e-06

GRADIENT TOLERANCE: nan

BRACKET: 0 nan nan nan nan

RESTARTING CONJUGATE GRADIENT ALGORITHM

The program then output the last 4 line endlessly. Anyone can point out what was the problem? Thanks a lot in advance.

Sincerely

Wei

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