Dear Amber users !
I still have a question about removing the periodic boundary conditions
(PBC) from membrane simulations. I used the autoimage command in cpptraj,
and it works well for keeping the protein centered in the box. However,
some lipids occasionally appear to rapidly jump back and forth across the
box boundaries, even over several nanoseconds, creating an unrealistic
effect in the membrane. Is there a way to fix this visual artifact with
additional options in cpptraj?
Many thanks in advance
Enrico
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Received on Thu Nov 07 2024 - 01:00:02 PST
