VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 26 2022 - 12:09:10 CDT

a few thoughts:
- you can create DCD files from LAMMPS directly using dump style dcd
- you can use the catdcd program instead of VMD to do the conversion
- please carefully check the first line of your VMD launch script. does it
have (#!/bin/csh or #!/bin/sh) as first line
  if the former, then checking for file size limits in a bourne shell with
ulimit may be misleading. You have to check with a c-shell, which may have
different limits configured by default.

On Thu, May 26, 2022 at 1:01 PM Dourna Jamshideasli <dzj0022_at_auburn.edu>
wrote:

> Dear VMD users,
>
> I would appreciate it if you could help with the “Filesize limit exceeded
> (core dumped)” error I am getting with VMD on Linux.
>
> I have VMD installed in both Windows and Linux environments. Using the
> Windows version of the VMD, I was able to save a lammpstrj file of around
> 19 GB as a DCD file of about 6 GB. However, when I do the same procedure
> in the Linux version, I get an error message of “Filesize limit exceeded
> (core dumped),” and only about 4 MB of the file could get saved.
>
> It is time-consuming to move files to my Windows and then do the
> conversion. Also, I need to do the same action for many cases, and it will
> take me ages to go through the VMD in Windows. After checking with our
> Network Service and using ulimit -a, I am sure there is no limitation on
> the file size creation. How can I use the VMD on Linux to store a file
> of a larger size?
>
> Thanks for your time and consideration.
>
> Thank you,
>
> Dourna Jamshideasli
>
> Ph.D. Candidate | MECH
>
> Pronouns: She/Her/Ms.
>
> dourna_at_auburn.edu
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7Q6A3_Hm6TmkM4JJ9smx-eTV8anQO5wj4rLkYPjfzyrMa1NnltDZgEmRNatIIlxThZEk0MrywTMsOMlbTg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.