VMD-L Mailing List

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Mon Aug 13 2018 - 00:03:23 CDT

Thanks for your reply! I couldn't find it but I downloaded a pre-compiled
version for linux and used it

On Sun, Aug 12, 2018 at 11:44 AM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> 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> 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
>> but don't really know how to install it (I have a windows computers).
>> Any help would be appreciated :)
>>
>> Regards,
>>
>> Sebastian
>>
>
>
>