[gmx-users] On the box type

[Tsjerk Wassenaar]

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.