VMD-L Mailing List

From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Fri Feb 24 2012 - 09:16:59 CST

Hi everyone,

I've experienced continuous increase of memory usage when I use pbc
wrap; e.g., if I run the following script where I keep wrapping a
trajectory around different atoms:

mol new testpsf.psf type psf
mol addfile testdcd.dcd type dcd waitfor -1
for {set ind1 0} {$ind1 < 1000} {incr ind1 1} {
   pbc wrap -molid top -centersel "index $ind1" -center com -all
-compound residue
}
(This is the entirety of the script, so the increased use of memory must
come from pbc wrap.)

I've read the manual and looked through the mailing list and found no
indication that I'm doing anything wrong. Can anyone help? I would
like solve this because I sometimes need to wrap a trajectory around
many different atoms and my scripts eventually crash due to lack of memory.

Thanks,

Ana