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 Å 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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