[gmx-users] Spherical shaped box

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 16 12:16:10 CEST 2012

Hi Sogol,

You remove jumps over periodic boundary conditions, giving a
continuous trajectory. That gives you a very nice view on diffusion in
your system, which happens to be equal in all directions. Hence, the
end result looks spherical. But that's not the same as having a
spherical box. If you draw the box in VMD or Pymol, you'll see it's
still close to the original (triclinic) shape, but has become a bit
small in relation to your molecules.



On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh
<kw_bagherzadeh at yahoo.com> wrote:
> Dear users,
> I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300
> K. after 1ns of simulation in 300 K, the protein jumps out of the box and
> when I use the command
>  trjconv_mpi  -f *.trr -s *.tpr -o *new.trr -pbc nojump
> followed by
>  trjconv_mpi -f  new*.trr -s *.tpr -o new*.pdb -dump 1000
> the box shape changes from dodecahedron to spherical. In Gromacs manual I
> read ;
> "  There are several possible shapes for space-filling unit cells. Some, as
> the rhombic dodecahedron and the truncated octahedron  approach a spherical
> shape better than a cubic box and are therefore more economical for studying
> an (approximately spherical) macromolecule in solution, since less solvent
> molecules are required to fill the box given a minimum distance between
> macromolecular images....... ".
> Does it mean that it is ok and I can continue the simulation or I have to
> increase the box size?  After simulation in 200 K the protein juped out of
> the box but using the same command the problem was fixed, without changing
> the box shape.
> Thank you in advance for the help
> Sogol
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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