Hi,
Sorry, when I said the box, I meant the box from the isosurface plotting.
My trajectory was obtained in implicit solvent, so no box.
I tried another approach:
center @* origin mass
volmap volmap.dx 0.5 0.5 0.5 .* centermask @*
go
And I obtained reasonable densities, as well as the expected spherical form.
Is that approach correct ?
Sincerely
Le 18/06/2016 à 13:33, Jason Swails a écrit :
> 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
>
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Received on Mon Jun 20 2016 - 05:30:02 PDT
