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 <raf...@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: raf...@us.es > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
