VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 08 2009 - 09:49:33 CDT

Hi,
  You should be able to use the "-minmax" parameter to control the
size of the grid, which will also set the number of grid points in
each dimension when combined with the "-res" parameter.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 08, 2009 at 01:22:22AM -0500, Jian Dai wrote:
> Hi, all:
> I'm doing analysis of water density above cholesterols in a lipid bilayer.
> Now I want to average the isosurfaces of water above all the cholesterol
> molecules in a frame, how can I do that?
>
> I was able to use "volmap density $selection -weight mass -o output.dx" to
> generate the dx file of water above individual cholesterols within a box and
> the command I used is like:
> "water and abs(x-$O6_x) <= $cutoff and abs(y-$O6_y) <= $cutoff and z >=
> $sys_c_z and (z-$O6_z) >= 0. and (z-$O6_z) <= $cutoff"", where cutoff = 10
> (Angstrom), and O6_x is the x position of a specific cholesterol oxygen,
> sys_c_z is the calculated z value of the center of the box.
>
> But the grid size is different for every cholesterol. In order to average
> over these data, I expect to have the same grid size for water molecules
> above each cholesterol. Is there a way?
>
> Thanks.
>
> Jian 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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