[gmx-users] Beginner Question -- Grab Info from Output

João Henriques joao.henriques.32353 at gmail.com
Thu Mar 10 09:40:20 CET 2016


I'm not sure I fully understand what you wrote. Do you want to catch the
output from gmx msd and store it in a file? If that's it, then you do
something like this:

gmx msd ... > filename 2>&1

The first ">" (or "1>") directs the standard output to the given file and
"2>" does the same thing but for the standard error. The extra "&1" tells
bash to store the latter in the same file as the standard output. In this
way, you're sure to store a faithful copy of the output you see in your
terminal in a text file.

To parse the file and get some values of interest, you can use a gazillion
different approaches. grep and/or awk would be good choices, but you don't
seem very confident with the terminal, so I guess it's better to stick with
a text editor.

Best regards,

On Thu, Mar 10, 2016 at 1:13 AM, ANAND AMITKUMAR DHARIA <
adharia at berkeley.edu> wrote:

> Hi,
> I am running gmx msd and would like to import the value of the calculated
> diffusion coefficient and error that is output in my linux terminal. I know
> I can view the trajectory with grace or parse the file in a text editor for
> its values, but I would just like end calculation. Is there a way I can do
> this? I can't seem to find the gmx program either in my computer.
> Thanks,
> Anand
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