[gmx-users] extracting individual particles properties

[Mark Abraham]

----- Original Message -----
From: Payman Pirzadeh <ppirzade at ucalgary.ca>
Date: Saturday, February 27, 2010 9:55
Subject: [gmx-users] extracting individual particles properties
To: gmx-users at gromacs.org

> This is the third time I am sending this e-mail, and I am
not sure why it does not show up on the list!!!!

It has shown up. Several times. Search the archives for previous answers.

> I have a simulation from which I have the .edr,  .xtc
and .trr files. I want to color my particles based on rmsd, potential energy,
Sg (tetrahedral parameter) or any other parameters in a specific configuration.
Is there a way to extract individual particle’s properties out of these
files? 

Some GROMACS tools can write PDB files that have the B-factor field filled with a relevant datum (e.g. atomic RMSF) but probably you"ll need to apply g_energy or other tools and your own scripting. Potential energy is a particularly useless thing to colour by.

Mark