[gmx-users] 3D solvent density distribution

[Matthew Watkins]

Hi all,

I would like to extract a 3D density distribution for particular species 
from simulations (not z averaged or slices).

My feeling is that g_sdf or g_spatial (v. 4.0.5 ) should be able to do 
this - the gaussian cube format would be ideal output for me - but I've 
not managed to fully understand the correct way of doing this. Using

g_spatialserial -f Mg_tip_over_O_1.xtc -s Mg_tip_over_O_1.tpr -n 
index.ndx -pbc

and selecting OW as a group 1 (TIP4P water) and system as group 2,  I 
get a grid.cube that superficially appears reasonable, but the 
simulation box is truncated and excludes volumes where the water is not 
present (slab simulation) and I would like to be able to plot substrate 
density at the same time.

How would I obtain a simple cube or similar file containing local 
densities and maintain the simulation box?

Cheers,

Matt

-- 
Dr Matthew Watkins
PDRA, London Centre for Nanotechnology
phone: +44 (0)20 7679 3436