Re: [ESPResSo] Re: Radius of Gyration

[Olaf Lenz]

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Hi!

Axel Arnold wrote:
> Apart from that, calculating a meaningful radius of gyration is non-trivial 
> in 
> your case. You cannot simply use the folded coordinates to calculate the rg, 
> because your cluster could also be located across a boundary. With folded 
> coordinates, that would look like two smaller clusters at the box boundaries.

I don't think that the problem is that hard. I see at least three
possible ways to solve the problem with not too much effort: on the VMD
level, on the ESPResSo level, or a combination using both.

1. Within VMD, you can use the pbctools plugin (which is part of VMD
since 1.8.6). Using the plugin, you can easily wrap all coordinates into
a unit cell which is centered around a particle (index 13 in this case):

        pbc wrap -sel "index 13"

If the compound does not stretch more than half the system size, this
will solve your problem.
When you have done that, you need to compute the radius of gyration. To
do that, you can either implement it within VMD (shouldn't be too hard),
or you can try to somehow write the coordinates to a file, read them
into ESPResSo and use it to compute the radius of gyration.

2. Alternatively, you can do the wrapping within ESPResSo and directly
use the analyze-command to compute the radius of gyration. To implement
the wrapping, you can try to go along the lines of the "pbcwrap" command
in the file "pbcwrap.tcl" in the attached plugin archive.
I think it would be pretty useful, if we had a Tcl proc that does the
wrapping in ESPResSo, therefore: if you implement it in ESPResSo, please
send us the resulting code that we can include it!
After December 15th, I would be willing to help.

Olaf
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pbctools-2.1.tar.gz
Description: GNU Zip compressed data