From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Apr 24 2007 - 09:49:59 CDT
This means that you have a set of starting coordinates that *cannot* be
minimized; the most frequent cause of this is having two atoms in
identical positions. You might want to visually inspect your structure
and make sure that nothing like this is going on, and that your box is
big enough.
Peter
Wei Liu wrote:
> 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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