On 8/06/2012 8:35 PM, Steven Neumann wrote:
Dear Gmx Users,
I pulled my ligand away from the protein and I found out that after
getting rid of PBC (trjconv -pbc whole)
There is no magic way to "get rid of PBC", and "-pbc whole" is certainly
not it. Read trjconv -h and see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for suggested workflows.
my ligand goes outside the box?
There is no outside. Since your ligand and your protein were probably
not part of the same [moleculetype], "-pbc whole" can't magically
understand you think they should be represented relative to the same
periodic cell. Correct usage of "-pbc cluster" might help.
Is it fine or should I increase my box as I want to run umbrella sampling?
We can't possibly know.
Mark
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