Re: outputname and restartname

From: Peter Freddolino (
Date: Tue Apr 07 2009 - 09:34:34 CDT

Hi Neelanjana,

Neelanjana Sengupta wrote:
> Hi Peter,
> --- I AM getting a .vel and a .coor file for abnormal termination of a
> simulation (I checked that again by forcibly killing one).

This sounds trivial, but... are you sure they weren't there before the
run started? And that these are not the restart.coor and restart.vel
files? If so, could you post the end of your config file (where you
actually do the run) and let me know where you terminated it?

> They are either pdbs (if binaryrestart is off) or namdbin files (if
> binaryrestart is on). The restart files are written every
> restartfreq steps, and can be used to restart a simulation that
> terminated abnormally. The information in those files is thus only
> redundant if your run finished successfully.
> ---- I do not have the binaryrestart option in my input file (hence yes
> by default), but I do NOT get any namdbin file!!

You shouldn't expect a .namdbin file, if that's what you're asking. It
sounded like you were asking for the format of those files, which I gave
you. Whether or not you have binaryrestart on, namd will write files
named $outputname.restart.coor and $outputname.restart.vel containing
the coordinates and velocities once every $restartfreq steps. These will
either be pdb files or namd binary files. It should also, at the end of
the run, write files named $outputname.coor and $outputname.vel, which
contain the final coordinates and velocities in either ascii (pdb) or
binary format depending on whether binaryoutput is on.


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