[gmx-users] RDF brads

Joe Jordan e.jjordan12 at gmail.com
Thu Mar 29 09:28:22 CEST 2018

You can just give the selection you would use to make the ndx file directly
to gmx rdf.

You should be fine to average the simulations RDF (and e.g. PCA) are
statistical properties, and averaging should give you better statistics =)

On Wed, Mar 28, 2018 at 11:56 PM, Alex <alexanderwien2k at gmail.com> wrote:

> 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
> RDF?
> Thank you.
> Best regards,
> Alex
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Joe Jordan

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