From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 20 2006 - 10:51:04 CDT
Hi Moumita,
the pressure values will be output repeatedly in your logfile, and they
are output exactly when they are calculated. You can judge the timing
based on your energy outputs; that initial energy and gradient output
that you posted, for example, is at the very beginning of minimization,
and you will get further output as the simulation proceeds.
The sync buffer overflow is an informative message about some memory
allocation, and is nothing to worry about.
Peter
Moumita Maiti wrote:
> 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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