From: Joshua Adelman (
Date: Wed Dec 22 2010 - 07:26:33 CST

Hi Aneesh,

As a general policy, you should not write personal emails to people who have responded to your questions on the list. We answer questions not just for your personal benefit, but for future users who (hopefully) read the archive.

In reply to your question, the simplest thing to do if the single trajectory is too big, is to split it into smaller pieces and run the script on each since they should be independent. You should also look into Bigdcd which might be a simple alternative.

Best wishes,

On Dec 22, 2010, at 6:29 AM, aneesh cna wrote:

> Dear Joshua Adelman,
> Sorry for writing a personal mail to you regrading a VMD query.
> Myself Aneesh, a graduate student from India. Thanking you for the valuable reply I got from you for my query in VMD mail list regarding the tcl scripting for counting water molecules around DNA.
> My simulation system contains DNA in a box of water and using Amber 9.0 for simulation. I wrote Tcl script to count the number of water molecules within 5 angstrom around DNA over the trajectories. I try to write the script in such way that at a time only one trajectory file will be consider. Even though the script is working fine, when I ran the script in command line mode its taking huge amount of RAM ( 3.5 GB out of 4 GB RAM) and the computer is getting hanged slowly.
> I have attached the tcl script for your reference. Please help me to figure out what exactly going wrong in my script.
> Thanks in advance
> Sincerely
> Aneesh
> <water.tcl>