[gmx-users] Problem: Protein move out of box

Pan Wu pan.wu at duke.edu
Thu Oct 8 23:41:02 CEST 2009

Hi Gromacs users,    I am new to Gromacs, and now setting up one very simple
system to test Gromacs+Martini. (one protein with solvent surrounded)
    When I run the MD and saw the trajectory, the protein seems go around
randomly, and across the box size. Because Periodic Boundary Condition, it
will come back from the other side. But I don't know *whether the across box
size movement will actually cause some problem about protein structure or

    In my mdout.mdp file, I can see:
        comm-mode = Linear
        nstcomm = 1
        comm-grps  =                      (default, should be system)

    Thank you in advance!


Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
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