FW: [gmx-users] Dynamical atom groups in 'index.ndx'

Berk Hess gmx3 at hotmail.com
Wed Jun 25 15:32:17 CEST 2008

From: gmx3 at hotmail.com
To: vvchaban at gmail.com
Subject: RE: [gmx-users] Dynamical atom groups in  'index.ndx'
Date: Wed, 25 Jun 2008 15:31:59 +0200


I think this would require complete rewriting of all the (required) analysis tools.
Currently all tools assume that you have a static, fixed length list of atoms.
You can not "simply" make this list dynamic.
It would be very useful to have such a functionality, but one would like to
have this implemented at a higher level.

There is currently a (limited) similar functionality via trjorder.
trjorder can order atoms based on distance. This effectively makes
you index group dynamic, but the size is fixed.
(although not for g_velacc, which needs time correlation, but there
it becomes difficult to define what you want to calculate exactly
with dynamic groups)


> Date: Wed, 25 Jun 2008 15:35:46 +0300
> To: gmx-users at gromacs.org
> From: vvchaban at gmail.com
> Subject: [gmx-users] Dynamical atom groups in  'index.ndx'
> Dear Colleagues,
> Did not anybody try to implement a possibility to use a changeable
> 'index.ndx' when analyzing a trajectory (g_rdf, g_velacc, etc)?
> I mean that the atoms numbers in 'index.ndx' could change,
> being different for different frames.
> This trick can be used for evaluating properties of molecules located
> in the definite area at the current moment. Now we can control the
> particles but how can we check if these particles are still located
> in the same area where they were before they started to move?
> Of course, one is able to do it by visualizing trajectory and then
> edit the particles number by hand but it is quite unlucky solution, as
> for me.
> Probably I'll try to make something like it if time permits.
> If somebody has got any considerations on this topic, please let me know.
> -- 
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svobody sq.,4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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