On Sat, Jun 18, 2016 at 6:38 AM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> 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 ?
>
If I had to guess, I would guess that you forgot to image your
trajectory. The density is normalized by the number of frames in the
trajectory, so if your particles are diffusing away from the central box
then the densities will appear artificially low.
Try using the "autoimage" command before the volmap command. Also, by
using "go" between the rms command and volmap, you may be wiping out the
effect of the RMSD command altogether. volmap is an action that operates
in the action stack on each frame at a time, so if you want to pass in the
RMSD-minimized frames to analyze those, you need to do it in the same stack
(i.e., do not separate them by "go").
HTH,
Jason
--
Jason M. Swails
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Received on Sat Jun 18 2016 - 05:00:02 PDT
