Re: outputname and restartname

From: Peter Freddolino (
Date: Wed Apr 08 2009 - 07:21:33 CDT

Yes, the restart files from the previous step are overwritten (actually,
moved to .restart.coor.old, and the previous .old files from 2 steps ago
are lost).

Neelanjana Sengupta wrote:
> 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,
> Neelanjana
> 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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