From: Moumita Maiti (m.moumita_at_gmail.com)
Date: Thu Jun 15 2006 - 15:59:50 CDT
Hi,
I have a molecule which consists of 267224 atoms. I gives the
following error(pasted at the end of the text) when I run conf file with
namd2.
I have two questions:
1. Is there a possibility that the problem is with psf file? I had some
warnings about some of the atoms when it was trying to guess the coordinates
for those.
2. I used 310K temperature and the other parameters like pirlist dist,
electrostatics..etc, just the values which were in the exaple file
"ubq_wb_eq.conf" of the tutorial.
3. How do you decide the periodic boundary values?
I understand some term is becoming infinity, I want to know the
possibilities which can cause this type of problem.
The error is:
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
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 93111.2340 -99999999.9999 13742.5589
18.4616
-2425107.4313 99999999.9999 0.0000 0.0000 0.0000
-99999999.9999 0.0000 -99999999.9999 -99999999.9999 0.0000
-99999999.9999 -99999999.9999 86856.0000 -99999999.9999 -99999999.9999
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
Thank you,
moumita
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