[gmx-users] minimum distance between the protein and its mirror image

[YanhuaOuyang]

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
        0        2.800  5.225  7.200  7.200  7.200
        2        2.793  5.136  7.200  7.200  7.200
        4        2.804  5.002  7.200  7.200  7.200
        6        2.777  5.176  7.200  7.200  7.200
        8        2.820  5.187  7.200  7.200  7.200
        10       2.871  5.043  7.200  7.200  7.200
        12       2.788  5.089  7.200  7.200  7.200
        14       2.882  4.892  7.200  7.200  7.200
       ................
        5154     4.153  3.415  7.200  7.200  7.200
        5156     4.222  3.483  7.200  7.200  7.200
        5158     4.154  3.608  7.200  7.200  7.200
        5172     3.607  4.124  7.200  7.200  7.200
        5174     3.556  4.140  7.200  7.200  7.200
        5176     3.303  4.430  7.200  7.200  7.200
        5178     3.291  4.297  7.200  7.200  7.200
        ...................
        5880     1.659  5.595  7.200  7.200  7.200
        5882     1.787  5.564  7.200  7.200  7.200
        5884     1.718  5.575  7.200  7.200  7.200
        5886     1.669  5.654  7.200  7.200  7.200
        5888     1.636  5.752  7.200  7.200  7.200
        5890     1.590  5.761  7.200  7.200  7.200
        5892     1.620  5.786  7.200  7.200  7.200
        5894     1.513  5.791  7.200  7.200  7.200
        5896     1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance between the outside of protein and the edge of box is 1.0 nm. the Minimum distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic image during simulation?
which group should I choose when i using gmx mindist, protein, C-alpha or some else?

Best regards,
Ouyang