Dear list,
I did a NPT study without setting iwrap=1, and find that water molecules are not in the box. From the archive I learnt that I can translate molecules back to the primary box using cpptraj. I tried the following command but found that the water molecules in the trajectory file are still messy.
trajin test.mdcrd
autoimage
trajout test1.mdcrd
is my command correct??
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Received on Tue Jul 05 2016 - 04:30:03 PDT
