[gmx-users] g_mindist , trajectory only CA atoms, to small values?

Shay Amram shayamra at post.tau.ac.il
Wed Dec 2 05:21:13 CET 2009

Bad choice of words. Did not mean to suggests there's actual program bug.

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Wednesday, December 02, 2009 00:46
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_mindist , trajectory only CA atoms, to small

t.peter.Mueller at gmx.net wrote:
> Dear Shay, dear Gromacians
>> For purposes of debugging this bug you can also use the flag of g_mindist
>> that gives out atom pairs and see which atom pairs is it that gromacs
>> thinks are less the 1 angstrom.
> I used the  "-o  atm-pair.out" option to get the atom pairs with the
> distance. For the all atom trajectory the correct atom pairs are selected.
> But for the CA trajectory the wrong atom pairs are selected. Instead of
> pairs with the shortest distance a much further pair is selected. Although

Can you post some of this output?

> the output pair from "atm-pair.out" has a distance of more then 100
> the value in  the file "mindist.xvg" is smaller then one Angstrom.

Is this for the CA-only trajectory?

> I think the "g_mindist" command has a bug. In the trajectory each residue
> only represented by a single CA atom (to reduce storage footprint and
> increase speed), can it be that g_mindist requires that the atoms have to
> "connected" (no broken bonds)? But for calculating the minimal distance of
> two groups this should really not be required.

Before we jump to the bug conclusion, can you post the command line you're 
using, groups you're selecting (are they custom? simply the default
and relevant snippets from the output and/or coordinate files that
demonstrate a 
bit better what's going on.  If, based on this information, things look
then file a bugzilla with files that reproduce the problem.  I would
that g_mindist requires bond information, since a .tpr file is not strictly 
required for its function.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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