[gmx-users] discrepancy between trjorder and g_dist ?

[Berk Hess]

>From: "Sandeep Somani" <ssomani at bii.a-star.edu.sg>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
>Subject: [gmx-users] discrepancy between trjorder and g_dist ?
>Date: Thu, 7 Oct 2004 18:06:16 +0800
>
>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 ?

No.
There is another problem with the distance in the pdb output of trjorder.
But only occurs for ordering molecules (not single atoms) where the distance
for some atoms can be slightly to large.

But in your case you have one single atom.

Are you sure that the order of the atoms in the pdb ouput still matches your 
index file?
trjorder can change the order of the atoms.

Berk.

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