[gmx-users] How do I redirect grompp errors to a file for parsing?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 1 20:37:58 CEST 2006

David Mobley wrote:
> So, this is probably a stupid question, but for some reason I can't
> figure out how to do it...
> I need to run a ton of small MD jobs for a whole bunch of different
> small molecules, some few of which have errors in their topologies
> which cause grompp to fail with an error. Therefore, I need some
> automated way of grabbing the output of grompp and parsing it to
> identify errors so that I can go back and track down the problems.
> However, I can't for the life of me figure out how to get grompp to do
> anything other than just print the errors to the screen. For example,
> standard things like:
> grompp (usual args) > file.dat
at least for csh >&
for sh it is more like 2>&1

man csh
man bash

> fail to redirect the errors.
> Any suggestions? I'm sure I'm missing something obvious.
> Thanks,
> David
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list