On 12/17/12 2:14 PM, zugunder wrote:
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
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.
OK, got it.
Justin Lemkul wrote
In the absence of the actual editconf commands, it's hard to judge the
utility of each of these setups.
The box vectors shown are the ones that will be used unless you manipulate
them in some way.
In this particular case the commands were:
g_editconf -f protein.gro -o protein_box.gro -bt triclinic -d 1.0 -c
and
g_editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.0 -c
and my concern is that the reported box volume in case of dodecahedron is
much bigger than that for a triclinic one (for the same protein). Sure, the
triclinic box volume is calculated from vectors 100% correctly, and I guess
that it is correct for dodecahedron as well
It is calculated correctly, the math is just a bit more complex (see the manual
for the equations). The distance to the box edge is defined the same way, but
the two approaches don't necessarily give equally suitable results. Consider
the first case, which produces a rectangular box from an elongated
configuration. If your protein rotates 90 degrees about the z-axis, you will
likely violate the minimum image convention, as the box vector along y is
insufficient to accommodate the protein. Problem! The dodecahedral box is
pseudo-spherical and thus, regardless of how the protein rotates, the minimum
image convention is not violated.
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)?
Justin Lemkul wrote
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.
So I need to run at least genion first. Got it.
Not genion, but grompp.
-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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