# [gmx-users] Wrapping molecules for octahedron box

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 12 11:12:20 CEST 2010

```Hi,

You might want to have a look at the pbc routines in src/gmxlib/pbc.c
in the gromacs source code. You'll have to translate it to Fortran
yourself though. Maybe Appendix C of
http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf
is also useful.

Cheers,

Tsjerk

On Wed, May 12, 2010 at 9:51 AM, Rafael Rodríguez Pappalardo
<rafapa at us.es> wrote:
> 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
> like
> RX(I) = RX(I) - BOXL * ANINT( RX(I) / BOXL)
>
> 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,
>
> Rafael
>
>
> --
> Dr. Rafael R. Pappalardo
> Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
> e-mail: rafapa at us.es
>
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--
Tsjerk A. Wassenaar, Ph.D.

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

```