[gmx-users] g_dist

[Kay Gottschalk]

I can also use VMD - not quite as comfortable as g_dist with the pbc  
problem solved, but probably the quick and dirty 'fix', since I will  
have to look at the trajectories anyway.
Thanks,
Kay.

On May 22, 2006, at 6:27 PM, Alan Dodd wrote:

> That'd certainly work if the movement is continuous,
> but if there are many fluctuations near the crossover
> point then sorting out which steps to fudge it at
> could be a pain.  Assuming you only care about the Z
> seperation, I'd be tempted to use g_traj to plot both
> groups, and subtract the z-position of one group from
> the other at each step.
>
> Just a thought.
>
> --- Xavier Periole <x.periole at rug.nl> wrote:
>
>> Kay Gottschalk wrote:
>>
>>> They are not interacting. The distance is larger
>> than 40 Å. But
>>> still,if the distance to the mirror image is 41 Å
>> and to the same
>>> protein in the box is 45 Å, the distance to the
>> mirror image will be
>>> plotted... We are indeed pulling on z.
>>> Best, Kay.
>>
>> Good, so the solution I proposed should solve your
>> problem !!
>>
>> XAvier
>>
>> -- 
>> ----------------------------------
>>  Xavier Periole - Ph.D.
>>
>>  Dept. of Biophysical Chemistry / MD Group
>>  Univ. of Groningen
>>  Nijenborgh 4
>>  9747 AG Groningen
>>  The Netherlands
>>
>>  Tel: +31-503634329
>>  Fax: +31-503634398
>>  email: x.periole at rug.nl
>>  web-page: http://md.chem.rug.nl/~periole
>> ----------------------------------
>>
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kay-Eberhard Gottschalk
Applied Physics and Center for Nano Sciences
Ludwig-Maximilians University
Amalienstr. 54
80799 Munich, Germany

Phone: +49-89-2180 3436