I recently wanted to see if steric clashes at the boundary of a molecular system I’m simulating might be responsible for high-velocity errors. I didn’t want to download the models with the periodic boundary specified because they are enormous, so I discovered how to explicitly specify a periodic box in VMD. My periodic box was centered at {-13.5 -19.5 6.0} and had dimensions of {1308.998 1278.998 1281.998}.
pbc set {1308.998 1278.998 1281.998} -all -molid top
pbc box -center origin -shiftcenter {-13.5 -19.5 6.0}
Not too hard. Hope it helps others looking to do the same thing.
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