[gmx-users] Re: Actual box size

Justin Lemkul jalemkul at vt.edu
Mon Dec 17 20:37:43 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list