From: Axel Kohlmeyer (
Date: Sat Sep 19 2009 - 09:55:57 CDT

2009/9/19 Thomas Evangelidis <>:
> Hi Katherine,
> lets say you want to count all the waters(TIP3) within 5 A of resids 1-50
> taking into account waters in the nearest periodic cells, then the command
> should be:
> llength [[atomselect top "(oxygen pbwithin 5 of (protein and resid 1 to 50))
> and resname TIP3"] list]


when giving code examples, please make sure that you give examples
of _good_ coding. this piece of code has a high risk of creating a memory leak
and is inefficient.

the same can be done by:

set sel [atomselect top "(oxygen pbwithin 5 of (protein and resid 1 to
50)) and resname TIP3"]
puts "found [$sel num] water molecules"
$sel delete

and this code uses the "num" option to do the counting in c rather
than creating a tcl
list and counting its length and show that the functions created by
atomselect have to
be deleted after use (it is better to always manually delete them
rather than counting
on tcl to clean up).

> I have an alpha version of a plugin to truncate trajectories and keep only a
> specified number of waters within R Angstroms of an atomselection, it might
> be helpful to your analysis.

that reminds me. having you been able to sort out your issues with bigdcd?
did the improved re-rentrant version of bigdcd work for you?

> regards,
> Tom
>> Dear VMD users:
>> My sytem contains 18 proteins in a unit cell. I also have several 20ns
>> trajectories (*.dcd) of this system.
>> I would like to calculate the distribution of the water molecules around
>> each one of the proteins and around the different amoinoacids that compose
>> them during the trajectories.
>> I've been trying to find another VMD mail list posted message containing
>> this question and somewhere in the VMD user's guide but I haven't found
>> anything related.
>> I've worked with some scripts in VMD, using the atomselect command and
>> doing
>> loops along trajectories.
>> What I need is some help with the right command to count water molecules
>> (TIP3) around a specific part of the protein.
>> Thank you in advance.
>> KP
> ----- End message from -----

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.