[gmx-users] Wrapping molecules for octahedron box

Rafael Rodríguez Pappalardo rafapa at us.es
Wed May 12 09:51:55 CEST 2010

On Wednesday 12 May 2010 05:38:50 Mark Abraham wrote:
> On 12/05/2010 2:27 AM, Sai Kumar Ramadugu wrote:
> > Dear Gromacs Users,
> >     I have a simulation of a protein in Truncated Octahedron box. I want
> > to calculate the water residence times and mean square displacements (of
> > water) around the active site residues. We developed our own algorithm
> > for doing the same.
> > In earlier simulations I had cubic box and anint() function was working
> Never heard of "aninit" and it's not in GROMACS.
> > for the periodic boundary conditions. Now that I have truncated
> > octahedron box, is there any function to my rescue? I searched the
> > gromacs forum and could not find any function. Is there any way to
> > circumvent this problem?
> There are various functions that deal with periodic boundary conditions.
> Search for pbc in the code.
> Mark
Dear Mark,
anint() refers to an intrinsic Fortran function which is used to apply PBC 

ANINT(X) returns the nearest integer to X converted to REAL.

The book of Allen & Tildesley shows how to use it for cubic boxes.
The program F.1 from it has code for PBC in various geometries. The subroutine 
TOBOUND could be the one Sai is looking for.

Best regards,


Dr. Rafael R. Pappalardo
Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
e-mail: rafapa at us.es
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