From: Axel Kohlmeyer (
Date: Wed Jun 06 2012 - 08:19:58 CDT

On Wed, Jun 6, 2012 at 3:09 AM, arun kumar <> wrote:
> Hi Axel,

please always send a copy of your mails to
the mailing list, so that others get to see how
the problem is resolved and the resolution is
archived so it can be researched later.

> As you said i ran VMD in debugging prompt, this time it didnt showed
> segmentation fault but stopped in between after reading some frames.

yes, it clearly tells you what the problem is:


> Info) Finished with coordinate file /root/Desktop/Cter-pep/pr2.gro.
> Info) Using plugin xtc for coordinates from file
> /root/Desktop/Cter-pep/MD50ns.xtc
> gromacsplugin) Error reading timestep, out of memory

here you are. you are running out of memory (or address
space, since you have a 32-bit binary and there you are
restricted to about 2GB address space per process even
though you have more RAM.

like john suspected, it is not a VMD problem.


> Info) Coordinate I/O rate 64.0 frames/sec, 42 MB/sec, 67.9 sec
> Info) Finished with coordinate file /root/Desktop/Cter-pep/MD50ns.xtc.

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.