Hi Jose, You're not the first one to follow the tutorial, it does state which version to use (4.5, see introduction), and it does state how to fix the topology: editing the file, adding the lines, using the appropriate names. This tutorial is made to be read and to be thought over.
Of course time flies. The tutorial was written a few years back and ion naming has changed. You should run genion with -pname Na -nname Cl these days. And you can use -p, but one of the aims of the tutorial is familiarizing you with the files, file formats, and components of a simulation. The error about the box has nothing to do with the tutorial anymore. You deviated from a well trodden path, editing the coordinate file, probably screwing it up... But please don't blame me for that. But I take note of the ion issue that hadn't been brought to my attentin yet. I'll fix it soon. Best, Tsjerk On Dec 7, 2011 8:31 PM, "Jose Borreguero" <borregu...@gmail.com> wrote: This tutorial doesn't seem to be quite useful, if so many errors pop up. Maybe it was implemented for Gromacs < 4.5.x but there's no info on the version it should be used. However, Lo and behold! I found that you have a nice page with Gromacs 4.5.x tutorials :D ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) I'll give a try with the Lyzosyme one! - Jose On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > Jose Borreguero ... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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