VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Wed May 06 2009 - 13:37:04 CDT

Hi all,

I am using vmd 1.8.7 alpha to run analysis on some desmond
trajectories. It works great, except when I try and run analysis on
several pieces of a long trajectory, it will crash on one of the last
few pieces with a message (extra lines included for context):

Info) Waters: 7578
Warning) Unusual bond between residues: 2 (none) and 3 (protein)
Warning) Unusual bond between residues: 310 (protein) and 311 (none)
Info) Segments: 1
Info) Fragments: 7672 Protein: 1 Nucleic: 0
Info) Using plugin dtr for coordinates from file
./BAR_HOMO_amber99.12/clickme.dtr
Failed to map file: Cannot allocate memory
Segmentation fault

I have the names of each trajectory piece listed at the top of the
script, then I use a foreach to loop over each piece one after
another. I think that the memory used to read each piece is not freed
after each iteration of the loop. Does that sound right? How do I do
the equivalent of rightclick->delete frames from within a tcl script?

Thx,
E