----- Original Message ----
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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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