From: lily jin (
Date: Thu Jun 07 2007 - 11:46:11 CDT

case 1:
I was writting a script. Because of some bugs it ran but only partly. So some file opened was not closed. When I tried to delete the file from the folder, I was told it was used.
case 2:
when I use 'lappend lista $h ' in my script, I want to be sure that lista is empty when I start to run the program. I can use 'set lista {}' . But when I have a lot of commands like this in the script, I wish to have a clean memory with one command.
I always want to have a clean memory before I ran a program.
When this happend, especially case 1, I had to close VMD and start it again.
'clear' is a command in Matlab which simply cleans the memory.
TCL has a command 'memory' which seems similar, however, it is not working in VMD1.8.5. I don't know if I made a mistake.

Thank you for helping!


----- Original Message ----
From: Axel Kohlmeyer <>
To: lily jin <>
Cc: VMD-L <>
Sent: Wednesday, June 6, 2007 2:35:17 PM
Subject: Re: vmd-l: release memory in TCL

On Wed, 6 Jun 2007, lily jin wrote:

LJ> While I run a program, all the data are saved in the memory. How can
LJ> I remove them to clear the system memory, like what 'clear' does in
LJ> MATLAB? Thank you!

there is not a single command in tcl, if i remember correctly.
but you can unset variables and arrays. they are also
cleaned up when used locally in a subroutine.

the most memory loss in VMD is usually due to trajectory
data (you can delete molecules to free that) and from
creating selections without deleting them.

other than that, it is easier to exit VMD and start over.

do you have a specific problem or can you describe a
scenario where something akin to 'clear' would be


LJ> Lily
LJ> ____________________________________________________________________________________
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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