Re: tcl script

From: Axel Kohlmeyer (
Date: Mon Feb 02 2009 - 23:01:26 CST

On Tue, 3 Feb 2009, wrote:

JA> Dear NAMD VMD developers:
JA> I have made a tcl script for analyzing two dcd files at the same time ( a
JA> trajectorie file and a velocity file), I have run the script in 16gb RAM

please note, that you are posting to the NAMD list,
but asking a question about VMD. there is a special
list for VMD, where your question is appropriate.

JA> computer but at some point the script always crashes, if I run the same
JA> script in my mac (2GB of RAM) I am getting the following error:
JA> vmd_MACOSXX86(1476,0xa040c720) malloc: *** mmap(size=36864) failed (error
JA> code=12)
JA> *** error: can't allocate region
JA> *** set a breakpoint in malloc_error_break to debug


JA> If you could give some hint about it, it would be great, I have attached the
JA> tcl script so you can look at it.

you are doing the #1 mistake when writing VMD scripts.
you create new selections with atomselect, but are
not deleting them. this will lead to a memory leak.


JA> Regards
JA> Jose Antonio
JA> PhD student

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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