darre...@ece.ubc.ca wrote:
Hi All,
I have an array of molecules above a grapehene sheet in my simulation.
However, when I look at my trajectory file (.trr) in VMD the array of
molecules is split into 4 sections with each section located at what
looks to be the corners of the simulation box. And the graphene sheet
does not stay stationary as it should, but rather jumps from corner to
corner. I tried to resolve this problem by running the following command:
trjconv -f traj.trr -o trajout.trr -center -pbc nojump
However, this did not resolve the problem. Is there something else I need
to do to resolve this problem?
No, some combination of options to trjconv should work. Sometimes two
two separate invocations with separate options are needed.
BTW "...does not stay stationary as it should" is not true... you're
wanting a certain feature for your visualization convenience, and during
the simulation GROMACS hadn't permitted you to choose which of the
infinite equivalent possibilities it should present in the trajectory.
You're choosing that now, *after* the fact.
Mark
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