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
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