Here, I have attached snapshot of my system after running energy minimization in NAMD. The problem that I continually have been facing is to see my system out of PBC box when I use the command pbc box. Are there any mistakes I have been doing so that I am finding my system out of pbc box ? or, is there are way to fit my solvated and ionized system inside the pbc box ?
Thanks
There is no any problem with your system, you can continue your work, but try to unwrap your systems, while you are analyzing your trajectories....
pbc unwrap -sel "protein" -all
Hi Roshan,
I am no expert in NAMD, but just a suggestion. I hope you can change these parameters in your Minimisation.namd file
# Periodic Boundary Conditions
> cellBasisVector1 65. 0. 0.
> cellBasisVector2 0. 53. 0.
> cellBasisVector3 0. 0 49.
> cellOrigin 8.35 69.64 -10.16
you can get this coordinate by using a tcl file.
Hope this works.
When you are running your system in a periodic boundary condition, it does not need to be sensitive to the position of the box.....
Thanks Ramin and Sneha. As Ramin pointed out, I guess I don't have to worry much about the position of the box when running my system in PBC.
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