Re: outputname and restartname

From: Peter Freddolino (
Date: Tue Apr 07 2009 - 06:12:59 CDT

Hi Neelanjana,

Neelanjana Sengupta wrote:
> 1. The 'outputname' corresponds to the .vel and .coor files written at
> the last simulation step. But what happens when a simulation stops
> unnaturally (say when a cluster crashes)? Am I right in assuming they
> still pick up the values from the last step that ran succesfully (and
> hence can be used in continuing the simulation)?
The .vel and .coor files are not written unless you successfully finish
a simulation. Quoting the manual entry on outputname
"At the end of every simulation, NAMD writes two PDB files, one
containing the final coordinates and another containing the final
velocities of all atoms in the simulation. This option specifies the
file prefix for these two files. The position coordinates will be saved
to a file named as this prefix with .coor appended. The velocities will
be saved to a file named as this prefix with .vel appended."
> 2. What are the binary filetypes written out with 'restartname' with
> the default 'binaryrestart' ? (They are presumably not .coor and
> .vel). Isn't the information in the restart files redundant if we
> already obtain the .vel and .coor files with outputname?
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.


> Thanks and regards,
> Neelanjana Sengupta

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