VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Thu Dec 10 2020 - 16:18:23 CST

Hello VMDers,

I am trying to generate a 'Total-potential.dx' from a constant e-field
simulation, where I need to add a linear potential to the
'Reaction-potential.dx' that would be generated by the volmap plugin. I
have looked through the documentation of voltool (which replaced volutil I
believe) to see if I could select a voxel by it's 3D coordinates. I am able
to get the size of the x, y, and z dimensions by using `voltool info xsize
-i input.dx` for each respective dimension. What I would like to do is loop
through every voxel, and add a z-dependent constant (linear potential). As
far as I understand, I am only able to add a constant to the entire
density, or select voxels near atoms, but not by their index [x y z].

I know this an be done in python, but I was hoping to keep the entire
script in TCL.

Thank you for your help, and advice.

______________
*Bassam Haddad*
R.L. Kirschstein NIH Fellow
Doctoral Candidate
Portland State University
Portland, OR