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
--
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
