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Dec 21, 2020 · $\begingroup$ @fireball. pbc wrap -compound fragment -center com -centersel "<enter your selection>: the chain(s) or molecule(s) you want to keep at the center of the box" -sel "<enter your selection>: the chain(s) or.

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dcd. I would also advice to just use the box information namd wrote to the dcd, what is actually really great as one have the whole history of the box size over time and can even watch the box shrinking during pressure. . . 5 -0. vmd.

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The procedures require the vmd unit cell properties # to be set.

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