[gmx-users] 3D solvent density distribution
matthew.watkins at ucl.ac.uk
Fri Aug 27 15:13:08 CEST 2010
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
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?
Dr Matthew Watkins
PDRA, London Centre for Nanotechnology
phone: +44 (0)20 7679 3436
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