AMBER Archive (2009)

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

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Mon May 18 2009 - 17:50:06 CDT

Thanks once again for your help Ross!

Bob Hopkins

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Ross Walker
Sent: Sunday, May 17, 2009 10:35 PM
To: 'AMBER Mailing List'
Subject: RE: [AMBER] Running PTRAJ command line scripts in background

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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