AMBER Archive (2009)

Subject: RE: [AMBER] Running PTRAJ command line scripts in background

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun May 17 2009 - 22:35:09 CDT

Hi Robert,

This is real easy to do. The key is that ptraj can read commands streamed
from standard input. So just put the commands you want into a text file (say
my_job.in). E.g.

trajin foo.mdcrd.1
trajin foo.mdcrd.2
trajout bar.mdcrd
...

Then run ptraj with:

$AMBERHOME/exe/ptraj < my_job.in >& my_job.out &

This will background the job and write all the output to the file
my_job.out.

If you want it to run even after you close the terminal then you just have
to prefix it with nohup. E.g.

nohup $AMBERHOME/exe/ptraj < my_job.in >& my_job.out &

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Hopkins, Robert
> Sent: Saturday, May 16, 2009 5:48 PM
> To: AMBER_at_ambermd.org
> Subject: [AMBER] Running PTRAJ command line scripts in background
>
> Amber Users,
>
>
>
> Hopefully, this is a simple question with a straightforward answer: Is
> there a way to run a Ptraj command line script (e.g., like the one on
> p.
> 82 of the AmberTools User Manual) in the background? I haven't found
> anywhere in the command that I can place an ampersand (&) and have it
> function properly (even if preceded by \ or placed in single or double
> quotes). If this can be done, I'd really appreciate knowing how.
>
>
>
> Thanks,
>
> Bob Hopkins
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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