[gmx-users] questions about trjorder

Yunfeng Hu yunfeng at scripps.edu
Sat Oct 16 01:32:17 CEST 2004

Thank you, Berk. This problem is now solved.

Best regards,

Date: Fri, 15 Oct 2004 10:57:29 +0200
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: RE: [gmx-users] questions about trjorder
To: gmx-users at gromacs.org
Message-ID: <BAY16-F22etD1ZdTr8g00020ade at hotmail.com>
Content-Type: text/plain; format=flowed

> 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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