[gmx-users] g_dist producing inconsistent values

[Alan Dodd]

----- 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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