[gmx-users] discrepancy between trjorder and g_dist ?

[Sandeep Somani]

Hi all

I am trying to understand the output of trjorder which "orders molecules
(in a group) according to the smallest distance to atoms in a
reference". 

i specified the group as a single atom (say A) and reference as another
atom B and ran trjorder on the trajectory file. the output pdb file
contains the distances in the B-Factor column. 

next, i used g_dist to find the distances between atoms A and B
expecting it to be same as that of trjorder. 
but got the following for the first 10 frames :


trjorder | g_dist
--------------------
2.76   |   3.2331  
2.73 	 |   2.8196  
2.70	 |   2.7658  
2.64	 |   2.7437  
2.51	 |   2.8133  
2.66	 |   2.6957  
2.68	 |   2.9658  
2.49	 |   3.3366  
2.57	 |   2.6732  
2.58	 |   2.9475  
2.85	 |   2.9758  

i am using ver 3.2.1. 

has anyone noticed this ? 

Thnx 
sandeep 


---
Research Associate
Computational Biology Group
Bioinformatics Institute 
Singapore

ph : 65-6478 8278 
fax: 65-6478 9047

http://www.bii.a-star.edu.sg/~ssomani

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