VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 23 2015 - 14:33:09 CDT

Max,
  I'm not entirely sure what it is you want out of the plot, so maybe you
can be more specific about what your input is and how you want it displayed.

Regarding the 'vol0' and 'interpvol0' atoms selection keywords:
  These select atoms according to the value of voxels in volumetric data
set 0. The 'vol0' selection samples only the "nearest" voxel to each atom
as the selection criteria. The "interpvol0" keyword does trilinear
interpolation among the 8 nearest voxels to each atom, and uses the
interpolated value.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 23, 2015 at 07:11:06PM +0000, Ebert Maximilian wrote:
> Hi there,
>
> I did implicit ligand sampling on my simulation and identified some channels. Now I would like to write plot the landscape along these tunnels from the bulk to the center of the protein. How could I do that? Also how can I get the energy value from the PMF in specific coordinate? I saw vol0 and interpvol0. What are the differences?
>
> Thank you very much,
>
> Max 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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