From: Pawel Kedzierski (
Date: Wed Aug 19 2015 - 09:23:22 CDT

A great tool to extract data from text files is awk, available in Unix
system (or gawk aka gnu awk otherwise).
With awk getting a a CSV spreadsheet from NAMD log file is a one-line
command like this:

awk '/^ENERGY:/{print $2, $11, $14}' OFS=, namd.log > spreadsheet.csv

This example will save columns 2 (TS), 11 (KINETIC) and 14 (POTENTIAL;
column numbers from NVE run) from lines starting with "ENERGY:" to file
spreadsheet.csv using comma as output field separator.
Extracting column heads and even the actual calculations can be done
with awk alone but such a simple example is easy to understand and
adapt, and you need to identify the column numbers anyway as they depend
on the calculations.

To extract all columns in a text file with (single line of) headers and
preserved column alignment, easily imported to Excel or Calc:

awk '/^ETITLE:/{if(h==0){print;h=1}};/^ENERGY:/{print}' namd.log > data.txt

A little more tricky example will give you all columns with headers as a
csv spreadsheet:

awk '/^ETITLE:/{if(h==0){$1="";print;h=1}};/^ENERGY:/{$1="";print}'
OFS=, namd.log > spreadsheet.csv

It will remove the labels from the first colums - a trick to make the
conversion of field separators in entire line.
This was actually tested with GNU awk as I work on linux.

W dniu 19.08.2015 o 03:38, Ern Seang Ong pisze:
> Hi VMD users,
> I have listed following questions about extracting data from NAMD log
> file.
> 1.I have run a simulation and I need to calculate the viscosity of the
> equilibrated system by using Green-Kubo relation. For the viscosity
> calculation, I need to the values of stress tensor (pressure in 3x3
> matrix), temperature and volume, which are available in the NAMD log
> file, but I do not know how to extract those values out into a
> spreadsheet.
> 2.Is there any way for me to export the graph as displayed in multiplot?
No idea what kind of graph you mean, but you can always extract the
plotted data from the Multiplot graph window, for example: File->Save as
ASCII matrix (this is a text file with aligned, space separated columns).

> 3.Is there any Tcl script available for viscosity calculation (using
> eg. Green-Kubo relations) in VMD?
> Thank you.
> Ernest
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