Re: Electron density profile?

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Dec 05 2008 - 01:59:05 CST

Dear Bin,

On Fri, Dec 5, 2008 at 1:40 AM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> I wonder whether there is a tool like "g_density" for GROMACS in NAMD,
> which would calculate the electron density of the system.

I've never used g_density myself, but from a quick look at g_density's
documentation, you may be able to do what you want by using the VMD
volmap command in one of the latest test versions:

volmap interp $sel -weight $list -allframes

where $list is a Tcl list containing, e.g., the number of electrons
for each atom in the selection $sel. If you run this with a trajectory
loaded, VMD will interpolate each atomic weight onto a 3-D grid for
each frame and average all the frames.

I'm not sure if this is what you are looking for. Alternatively, you
can convert your .dcd trajectory to .trr using catdcd, but it seems
that you'll need to create a .tpr structure file to be able to run
g_density.

Best,
Leo

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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