radial distribution function

[Takahiro Ohkuma]

Dear developers and users

I am trying to make CG potentials for a homo-polymer system with IBI.
I found that the radial distribution function of CG beads calculated with csg_stat shows different results when the bonded (angles / dihedrals) interactions are defined or not in the mapping xml file. I guess some neighbor beads are automatically excluded in calculating the RDF, and this rule should hold in the IBI process. Is it right? How can I control the exclusions?

Thank you very much.
Takahiro Ohkuma

[Christoph Junghans]

Hi Takahiro,

this topic comes up again every now and then and has been discussed on
the mailing list extensively on the mailing list.
A good summary can be found here:
<https://groups.google.com/d/msg/votca/3P8iT9UVBHg/gSTigVSQAwAJ>

In short, bonds, angles etc. in the mapping file generate exclusion
automatically, in the same way as gromacs does.
You can use
$ csg_dump --top topol.tpr --cg map.xml --execl
to figure out what VOTCA is doing.

Cheers,

Christoph

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--
Christoph Junghans
Web: http://www.compphys.de

[Takahiro Ohkuma]

Dear Christoph

Thank you very much for your quick reply.
I will follow your link first.

Best regards
Takahiro

2016年4月25日月曜日 17時30分02秒 UTC+2 Christoph Junghans: