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

[ANAND AMITKUMAR DHARIA]

Thank You! New to linux and still trying to understand the syntax. Much
appreciated!

Best,
AD

On Thu, Mar 10, 2016 at 12:40 AM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> Hi!
>
> 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,
> J
>
>
> 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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