Hi,
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.
Cheers,
Patrick
Alan Dodd a écrit :
----- Original Message ----
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Thursday, February 7, 2008 6:35:55 PM
Subject: Re: [gmx-users] g_dist producing inconsistent values
[EMAIL PROTECTED] 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
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
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