On 12/17/12 1:48 PM, zugunder wrote:
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?
In almost all cases, a dodecahedral box is the optimal choice. A cubic box with
the same periodic distance for an elongated protein would be much larger.
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)
In the absence of the actual editconf commands, it's hard to judge the utility
of each of these setups.
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)?
The box vectors shown are the ones that will be used unless you manipulate them
in some way.
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)?
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc mol
-ur compact.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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