VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed May 06 2009 - 13:48:12 CDT

Dear Edward,

On Wed, May 6, 2009 at 1:37 PM, Edward Lyman <edward.lyman_at_gmail.com> wrote:
> 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?

You can use the 'animate delete' command.

Cheers,
Leo

>
> Thx,
> E
>
> 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign