[gmx-users] RDF

Peter Kroon p.c.kroon at rug.nl
Tue May 22 10:54:31 CEST 2018

Hi Alex,

we have at some point looked at this in the group, but results were
disappointing IIRC. The approach we tried was basically clustering water
in groups of 4, but then you get tripped up by 1) PBC and 2) isolated
water molecules in an active site (or something). Either way, this isn't
something Gromacs can (or should) deal with; have a look at MDAnalysis
if you want to go down this path.

And I would like to redirect you to the forum of cgmartini.nl, where
there's more Martini specific knowledge.

Peter from the Martini group

On 18-05-18 21:42, Alex wrote:
> Dear all,
> I wan to parameterize the interaction between coarse-grained beads of a
> molecule and beads of P$ martini water using Votca. So, I want to calculate
> the RDF between moecules's beads and water beads in atomistic level as
> target RDF.
> I know the mapping of the molecule itself so that I know how to calculate
> the RDF between molecule's beads in atomistic level easily, but my problem
> is with calculation the RDF between molecule's bead and water bead, as I do
> not know the mapping of water, so, I wonder if one could help me calculate
> the RDF between molecule's beads and water?
> Thank you.
> Alex

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