VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Thu Feb 21 2019 - 16:02:08 CST

Thank you both for the response!

I already have MDAnalysis installed on my computer, so this will be easy to
work with!

On Thu, Feb 21, 2019 at 12:22 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Bassam,
>
> I'm unaware of a plugin to do this, but if you like python,
> GridDataFormats (https://www.mdanalysis.org/GridDataFormats/) has the
> tools you need to turn a .dx file into a numpy array that you can slice
> however you like and either plot directly in matplotlib or export it to a
> format that your preferred plotting utility uses.
>
> -Josh
>
>
>
> On 2019-02-21 12:45:41-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hi Everyone,
> I am working with ion channels, and using constant E-Field simulations. It
> would be nice to plot the voltage as a function of the z-axis, however I am
> unsure how to retrieve this information from the volumetric .dx file. Is
> there a VMD plugin available to extract this info, or will I have to write
> a script. If the latter is the case, could someone point me in the right
> direction?
> Thank you,
> Bassam
>
>