[gmx-users] Actual box size

[zugunder]

Hi,

I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered globular enough to try dodecahedron box?

Out of curiosity, I compared the triclinic and dodecahedral boxes created
for my protein.

After I created a triclinic box with g_editconf, I got this:

Read 2406 atoms
Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
    system size :  4.830  3.541  4.901 (nm)
    center      : 19.439-14.327 13.948 (nm)
    box vectors :  4.830  3.541  4.901 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  :  83.82               (nm^3)
    shift       :-16.024 17.097-10.498 (nm)
new center      :  3.415  2.771  3.451 (nm)
new box vectors :  6.830  5.541  6.901 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 261.17               (nm^3)

Dodecahedron:

Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
    system size :  4.830  3.541  4.901 (nm)
    diameter    :  5.907               (nm)
    center      : 19.439-14.327 13.948 (nm)
    box vectors :  4.830  3.541  4.901 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  :  83.82               (nm^3)
    shift       :-13.508 20.257-11.153 (nm)
new center      :  5.931  5.931  2.796 (nm)
new box vectors :  7.907  7.907  7.907 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 349.61               (nm^3)

So from the box volumes I see that in this case a triclinic box is a
preferred choice. However, as I am aware that dodecahedral box
representation (as seen in VMD for example) is subject to periodicity
effects, I am not completely sure if exactly these box sizes will be used in
simulations. If not, how could I estimate the actual box volumes before I
start simulation (to maximize performance)?

And I have one more short question:
Is it possible somehow to visualize the "actual" dodecahedral box at this
stage (i.e. right after adding water, having no trajectory file yet)?

Thank you.



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