Re: outputname and restartname

From: Neelanjana Sengupta (
Date: Tue Apr 07 2009 - 23:23:48 CDT

Hi Peter,

OK, I got it. The files I got were the restart files (I used the same
outputname and restartname).

Just one last conformations: The restart coordinates/velocities written at
the latest step overwrite those at the previous step, right? (Since I've
found that the filesize does not increase with either restartfrequency or
with the simulation length).

Thanks a lot,

On Tue, Apr 7, 2009 at 8:04 PM, Peter Freddolino <>wrote:

> 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.
> Peter

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