VMD-L Mailing List

From: Sonibare, Kolawole (kasonibare42_at_students.tntech.edu)
Date: Mon Sep 10 2018 - 14:13:34 CDT

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".
  2. 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.