[gmx-users] RDF brads

Alex alexanderwien2k at gmail.com
Wed Mar 28 23:57:26 CEST 2018

Dear all,

To obtain the coarse-graine (CG) parameters of a molecule using votca,
below are the considered beads: (the bead are weighted by atomic weights )
Bead A contains atoms of " a1, ..., a11"
Bead B contains atoms of " b1, ..., b9"
Bead C contains atoms of " c1,..., c13"

Now, to calculate the RDF (A-A, A-B, A-C, B-C, B-B and C-C), in the all
atom gromacs, would you please confirm me that I have to bundle the atoms
of a1, ..., a11 in index.ndx (gmx make_ndx) in a section called A (and for
the rest as well), and then using gmx rdf -ref A -sel B ... I am able to
calculate a RDF similar to what I get in CG?

One more question:

Since the molecule which I was talking about in the last question is a log
polymer which is hard to move and also I considered to have 300 molecules
of that in my all atom MD system, so, I did not simulate my system for a
long time (25 ns), but rather I simulated the system in multiple short MD
simulation (5 * 5 ns), each with different initial conf.gro (but all
include 300 molecules), now, I was wondering how can I calculate the
physical quantities of the system out of those simulation? for example for
the RDF, can I average the RDF of the 5 short simulations to get the final

Thank you.
Best regards,

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