Re: Concatenating log files

From: Brian Radak (
Date: Wed Sep 06 2017 - 11:32:02 CDT

Self-promotional plug:

I'm sure NAMD plot is very nice, but if you want to use other graphing
programs you can also use the PyNAMD Python package started by me on

PyNAMD is a lightweight object oriented take on NAMD files, particularly
the output log. The current distribution also includes some simple
analysis scripts that don't require any additional programming. For
example the "namd2flatfile" program takes any number of log files and
converts the ENERGY: entries to a simple flat column format. You can
also control the number of entries with the usual start/stop/step syntax
and pare down the output by directly selecting the quantities by their

Feedback on the project is welcome. The package might also eventually
make its way into the standard NAMD distribution as it is currently
being extended to support several more complicated analyses.


On 09/06/2017 11:14 AM, Vermaas, Joshua wrote:
> Wouldn't something like "cat log1.log log2.log > concatenated.log" work? Its been a while since I've used NAMD plot, but I think it ignores header-like things and only looks for lines that start with "ENERGY"
> -Josh
> On 09/06/2017 10:13 AM, Roshan Shrestha wrote:
> Dear all,
> I extended the previous simulation in NAMD, so now I have two log files for the previous and current MD simulation. Since I use NAMD plot to plot my data, is there any way to concatenate these two log files into one log file.
> Thanks
> --
> Roshan Shrestha
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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