[gmx-users] On the box type

[akcyrus]

Dear all and Tsjerk Wassenar,
I could not grasp how a rectangular box will be a problem. Lets assume a I
have a cylinder of radius r (nm) and height h (nm) with h>r. I place the
cylinder aligned along z-axis and then in a rectangular box with dimension
2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem
could be when during simulation, the cylinder gets aligned parallel to XY
plane and the box vectors are shorter along X and Y,isn't that right? Also
during the simulation, with isotropic pressure coupling the box tend to be
cubic and this would also cause problems. Correct me if I am wrong or don't
understand it right.
regards,
akcyrus


On Sun, Jul 7, 2013 at 12:00 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Cyrus,
>
> In a rectangular box (which is a specific case of a triclinic box) your
> molecule can't rotate freely without significant chance to run into its
> periodic image, invalidating whatever result you get. So, unless rotation
> is of no concern, or can be cirrcumvented, you'll need to use a rhombic
> dodecahedron.
>
> Cheers,
>
> Tsjerk
>
>
> On Sun, Jul 7, 2013 at 11:25 AM, akcyrus <akcyrus at gmail.com> wrote:
>
> > Dear all,
> > I am planing to do pulling on a bundle of elongated proteins. I compared
> > two box types - triclinic and
> > dodecahedron. The volume and total number of atoms (protein+solvent),
> > following the editconf and genbox commands,
> > were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 242222
> for
> > dodecahedron.
> > Although dodecahedron box has always been suggested due to shortcomings
> in
> > the periodic interactions for a triclinic box, but
> > I have seen examples of the use of triclinic box. Due to this huge
> > difference in the number of solvents in the two cases
> > I am tempted to use triclinic box, but I am a bit confused. Any ideas or
> > suggestions?
> > regards,
> > cyrus
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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