Hello,
I would like to use the volmap command to get "a density" for all the
atoms of my trajectory. I used the following commands (in cpptraj):
[...]
rms ref [1us] mass out rms.agr # Perform a rmsd on the frame at 1µs
go
volmap volmap.dx 0.5 0.5 0.5 .* centermask .*
However when I try to visualize volmap.dx, I observe that the densities
are very low (~1e-05). Moreover, while I expected the density to have a
spherical form, I just get a random one. It's like the rmsd didn't work,
and I just observe my molecule passing through the box.
Do you have any idea why I get this result ?
Sincerely
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Received on Sat Jun 18 2016 - 04:00:03 PDT
