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Re: [ESPResSo-users] Quick way to follow the aggregation of molecules ov

From: Olaf Lenz
Subject: Re: [ESPResSo-users] Quick way to follow the aggregation of molecules over time
Date: Fri, 17 May 2013 08:34:33 +0200
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Hi Koen!

Sorry for the later reply.

On 04/17/2013 06:01 PM, Koen Nickmans wrote:
> To do this, I would like to calculate the distances between the 
> center of mass of several molecules (with mol-id's defined). Is
> there a command like: analyze centermass _mol-id, _as opposed to
> the similar command for particle types listed in the UG?

No, there isn't. One of the problems of the various analyze commands is
that each of them uses a completely different way to specify which
particles it should use.
However, I think it should be pretty simple to extend the command such
that it can also handle mol ids.
Of course, you can also do it in Tcl, using "analyze set" to get the
molecules, "part $pid print pos" to get the coordinates and then
computing the COM.

> Alternatively, the minimum distance between any particles
> belonging to different mol-id's would be great too. However, I
> cannot find much in the user documentation about what one can do
> after having set mol id's in the first place.

So far, the main use of the mol ids are the commands from section 8.2.1
(Analyzing groups of particles), which are mainly intended for polymer
simulations. Otherwise, the mol id is not really used a lot.

> I guess the analyze aggregation command would work too. However I 
> would like to follow the distances between the molecules over
> time.

Have a look at the code of "analyze aggregation", it should be simple to
get what you need from it.


- -- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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