[gmx-users] questions about trjorder

Berk Hess gmx3 at hotmail.com
Fri Oct 15 10:57:29 CEST 2004

>From: Yunfeng Hu <yunfeng at scripps.edu>
>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] questions about trjorder
>Date: Thu, 14 Oct 2004 16:30:40 -0700
>Hi, I am trying analyze the distance change between a ligand atom and the 
>surrounding waters. I first used make_ndx (> 12 & a 2391) to define this 
>atom and then use trjorder to generate a pdb file that includes all the 
>"reordered" water molecules besides the protein and the ligand. As the 
>manuscript claims that the last column of this pdb file represents the 
>referred distance. However the distance between atom 24326 OW and atom 2391 
>C2 is 3.55 angstrom. What does 1.79 stand for here then?

For the distance (in nm) to the first atom in the system.
This is a bug which has been reported before, also a week ago,
but I was not able not locate the bug. This was because I always
tested with a reference group which included the first atom.

The following change in src/tools/trjorder.c will fix the problem.

<         pbc_dx(x[order[i].ref],x[order[i].i+j],dx);
<         top.atoms.pdbinfo[order[i].i+j].bfac = norm(dx);
>         top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d);


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