[gmx-users] g_dist producing inconsistent values

Patrick Fuchs Patrick.Fuchs at ebgm.jussieu.fr
Fri Feb 8 10:37:23 CET 2008

another quick and dirty tip (but at least it works !) is to generate a 
new trajectory using trjconv with a huge layer of vacuum on the Z 
direction (assuming your membrane normal is oriented along Z): you can 
do that with the -box option with a large value for Z. If you just put 
only the phosphorous atoms in there this won't generate a large file.


Alan Dodd a écrit :
> ----- Original Message ----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, February 7, 2008 6:35:55 PM
> Subject: Re: [gmx-users] g_dist producing inconsistent values
> chris.neale at utoronto.ca wrote:
>>> I've since found the source of my problem - the program was measuring 
>>> the (marginally shorter) distance across the PBC boundary, rather than 
>>> the distance
>>> within the box.  Unfortunately there doesn't seem to be a way to turn 
>>> PBC images off (correct me if I'm wrong?), so I guess I'm going to do 
>>> some jiggerypokery with the data and some math.
> Distance larger than half a box size are ill-defined anyway in a PBC 
> simulation. 
> -What do you mean?  I'd assumed that simply having enough water separating a bilayer from its periodic image that no water 'saw' both bilayers would be sufficient; is this not the case?
> In some special cases you can do this, for instance within a 
> protein it would work. I've implemented -nopbc options in some programs 
> but not in g_dist yet. Please put it on the developer wishlist. on the wiki.
> -Done.  Until then, I'm using g_traj -ox -com and doing the math with my own script.  Many thanks for the various alternative techniques suggested.
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Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
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Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
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