VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sun Aug 12 2018 - 10:44:49 CDT

It’s pre-compiled for unix-like platforms, but I don’t know if that’s true for Windows. Do you see anything here?

plugins/${ARCH}/bin/cionize1.0/cionize

If not, then you or someone else would have to compile it.

As for how to run it, you create an input file (cionize.in for instance) containing something like

> R_ION_SOLUTE 5
> R_ION_ION 5
> BORDERSIZE 10
> GRIDSPACING 0.5
> BEGIN
> PLACEION MG 1822 2
> SAVEION placed_ions2.pdb

And then call it using "cionize -i cionize.in YOURSYSTEM.pqr”. Note that VMD can write PQR files once you’ve loaded a PSF and a PDB.

Best,
JC

> On Aug 10, 2018, at 2:35 AM, The Cromicus Productions <thecromicusproductions_at_gmail.com> wrote:
>
> Also, could someone give me an example of how to cionize a dna molecule for example with 10 potassium ions?
>
> On Fri, Aug 10, 2018 at 3:07 AM, The Cromicus Productions <thecromicusproductions_at_gmail.com <mailto:thecromicusproductions_at_gmail.com>> wrote:
> Hello,
>
> I'd like to use cionize but it doesn't appear as a plugin. I found it on github
> https://github.com/thatchristoph/vmd-cvs-github/tree/master/plugins/cionize <https://github.com/thatchristoph/vmd-cvs-github/tree/master/plugins/cionize>
> but don't really know how to install it (I have a windows computers).
> Any help would be appreciated :)
>
> Regards,
>
> Sebastian
>