Regarding box-size

From: Moumita Maiti (m.moumita_at_gmail.com)
Date: Tue Jun 20 2006 - 06:32:43 CDT

Hi Peter,

                   I have few questions about the output data in the log
file which is the output of the run of the conf file.:

1. The minimization is done first before any MD simulation is performed. The
output file *.log prints energies and
pressures during minimization. The printing during minimization before
performing any simulation in log file is as
follows what I have got:

TCL: Minimizing for 5000 steps
[0] Info:: Sync buffer overflow and expanded!
[0] Info:: Sync buffer overflow and expanded!
[0] Info:: Sync buffer overflow and expanded!

I ran the example file for ubiquitin where the above ouput data are absent
in the log file. Is this a warning to have this type of info? What does the
"Sync buffer overflow and expanded!" mean?

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

Is the printing value of pressure above the calculated one after 5000 steps?
Does it depend on initial psf and pdb
file used as input for the molecule?

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
-871525.7046 99999999.9999 0.0000 0.0000 0.0000
-99999999.9999 0.0000 -99999999.9999 -99999999.9999 0.0000
-99999999.9999 -99999999.9999 10648000.0000 -99999999.9999 -99999999.9999

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan

Is the gradient tolerance calculated after 5000 steps, or is it done
before performing minimization?

Thank you,
sincerely,
moumita

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