Pan Wu wrote:
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.
Whether that's reasonable depends how much time is elapsing between the
frames. You may also wish to use trjconv to center each frame on some
suitable group - e.g. your protein. See trjconv -h and play around with
the options. mdrun doesn't bother making the output look "nice" since it
doesn't know what you think "nice" is. :-) It will only write molecules
that are "broken" across PBC only under some awkward algorithm
combination, however.
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 dynamics*?
In my mdout.mdp file, I can see:
comm-mode = Linear
nstcomm = 1
comm-grps = (default, should be system)
Should be fine.
Mark
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