VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 12 2018 - 23:50:14 CDT

On Mon, Sep 10, 2018 at 3:36 PM Sonibare, Kolawole <
kasonibare42_at_students.tntech.edu> wrote:

> Dear all, I am trying to convert a lammps trajectory file (.lammpstrj) to
> a gromacs trajectory file (.trj). I am trying to use catdcd to do this but
> I have a couple of problems.
>
> 1. The documentation says there would be a make file in the downloaded
> precompiled binaries, but there is nothing except the executable.
> Apparently, there has been some queries about this but I can't find any
> resolution of the issue. So I tried to instead to instead add the path of
> the executable to the .vmdrc file the way I would install a plugin. This
> didn't work too because when I type "catdcd" in my terminal, I get "command
> not found".
>
>
.vmdrc doesn't help. you have to add this to your general path for your
shell. hence the error.

>
> 1. Then I proceeded to run the executable directly. Whenever I try to
> do this, I get this error message:
> CatDCD 4.0
> Opening file 'abc.dcd' for writing.
> Opened file 'dump_abc.lammpstrj' for reading.
> Segmentation fault (core dumped)
>
>
> The lammpstrj file is just about 700MB and contains about 20,000 frames. I
> have 32gb RAM on my workstation and over 1tb of space.
>

this looks like an error in the command line. since you don't provide it,
nobody can help you.

axel. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.