Hi,
What format is 'mol.coord'? Does it contain box info? No periodicity
would lead to the RDF decaying to 0.0. If not, can you please post
your complete cpptraj output? Thanks.
-Dan
On Wed, Nov 14, 2018 at 5:11 AM <diego.soler.uam.es> wrote:
>
> Hello All,
>
> I am trying to extract a Radial Distribution Function (RDF) from a
> simulation. My topology and parameter file is mol.prmtop, and my
> coordinate file is mol.coord. The system is basically a DNA with a lot
> of waters around. I want to compute the RDF of waters with respect to
> a particular atom, atom number 179. I am using this script:
>
> parm mol.prmtop
> trajin mol.coord
> radial RDF 0.1 100 :WAT .179
>
> and running it with "cpptraj -i cpptraj.in". But the result looks
> very weird, because the RDF goes to zero instead of going to one, so I
> guess I am doing something wrong, but I cannot fix it.
>
> Thanks in advance for your help!
> Diego
>
>
>
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Received on Wed Nov 14 2018 - 16:00:03 PST
