Re: outputname and restartname

From: Neelanjana Sengupta (
Date: Tue Apr 07 2009 - 07:45:07 CDT

Hi Peter,

Thanks for your reply. However:

On Tue, Apr 7, 2009 at 4:42 PM, Peter Freddolino <>wrote:

> 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."

--- I AM getting a .vel and a .coor file for abnormal termination of a
simulation (I checked that again by forcibly killing one).

>> 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.

---- I do not have the binaryrestart option in my input file (hence yes by
default), but I do NOT get any namdbin file!!

Could you please point out what's going on? I am using NAMD 2.6.


> Peter
> Thanks and regards,
>> Neelanjana Sengupta

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