[gmx-users] discrepancy between trjorder and g_dist ?

[Sandeep Somani]

> 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.

am not sure if i understood you. still .. 

because i have a single atom in both the groups, there is nothing to
order and the only non-zero b-factor entry in the pdb frames is the one
for atom B. and the order of the atoms in the output pdb frames is
exactly the same as the original gro/pdb file. 

-sandeep



> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
> Sent: Thursday, October 07, 2004 8:59 PM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] discrepancy between trjorder and g_dist ?
> 
> 
> 
> 
> >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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