VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 05 2008 - 21:54:46 CST

>
> Finally, I was actually thinking of using this idea of partitioning the
> space in different "spherical slices" to see if there is some gradient
> in the number density of water in the vicinity of the peptides. I don't
> have a clear idea about how to do this at the moment ... any suggestions ?

you can use the volmap tool (after aligning the peptide over the trajectory)
and then use isosurfaces or a volume slice.

cheers,
    axel.

>
> Best
> Giovanni
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.