[gmx-users] editconf and g_rmsdist

Enemark Soeren chees at nus.edu.sg
Thu Sep 24 12:17:18 CEST 2009

Dear Tsjerk,
Thanks for your suggestion. I tried changing the box values, and it still give a deviation, so I have filed a bug report.

Best regards,

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Friday, September 18, 2009 7:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf and g_rmsdist

Hi Soren,

>  Why I am seeing this difference? Is it due to round-off's after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
> wrongly?

It's a bit weird indeed. You might be right that it's due to round-off
errors. You can try to copy the original gro file and replace the last
line with "   4.00000   4.00000   4.00000" to set the box manually.
That should rule out whether it's the box, which I can hardly imagine.
The other test is to add a shift, but you'd want to make sure that
rounding could get an issue then...

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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