VMD-L Mailing List

From: Guanglei Cui (cuigl_at_psu.edu)
Date: Thu Aug 11 2005 - 12:32:32 CDT

Hi,

The python looks something like this ...

import ....
import ...

for frame in range(0, 10):
   set_frame(0, frame)
   closewat = AtomSel("resname CGW and all within 5 of resid 1 to 8000",
0, frame)
   print frame, len(closewat)

In the first place, I thought it was memory issue because my trajectory
file is quite big. Then I found out it only happens to some frames. The
script wouldn't work even if I only have one such frame loaded. However,
all of this was observed with VMD on OSX (512MB memory). In windows ( a
machine with a 1GB memory), this didn't occur. The equivalent Tcl script
worked fine for the problematic frame I tested. So at this point, I
don't know what causes this. Thanks.

Regards, 

--
Guanglei
John Stone wrote:
> Hi,
>   Can you show us the Tcl or Python code that you used that crashed VMD?
> Is it possible that you're eating up all of your machine's memory and VMD
> is crashing as a result of running out of memory?
> 
>   John Stone
>   vmd_at_ks.uiuc.edu
> 
> On Thu, Aug 11, 2005 at 11:55:39AM -0400, Guanglei Cui wrote:
> 
>>Hi,
>>
>>I am trying to calculate the close residues using VMD for a trajectory I 
>>have. However, at one frame, VMD crashed. I tried to do this through 
>>python and tcl interface. Both failed at the same frame. However, if I 
>>did it in the Graphics Representation dialogue, it worked fine. I'm 
>>using VMD 1.8.3 (Feb 15, 2005). Your help is greatly appreciated.
>>
>>Regards,
>>
>>--
>>Guanglei
> 
>