On 14/06/2012 5:47 PM, Shima Arasteh wrote:
Dear gmx friends,
I put a protein in a simulation box filled of water molecules and
entered the mdrun command. After the simulation, I found the protein
near one of the edges of the box and not in center. What is the
problem? Anyone may suggest me?
Does it mean that the simulation is meaningless?
I expect the protein to stay in the center of box and goes unfold by
passing the time.
See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
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/Support/Mailing_Lists/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/Support/Mailing_Lists
