[gmx-users] Pulling - ligand outside the box

[Mark Abraham]

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