I have a question regarding the "update" command.
As long as I am not interested in nonbonded properties like H-Bonds and other electrostatic stuff is it safe to ignore the update command?
Lets say I read the trajectory without setting up the crystal information, iterate it step by step while re-centering every step and then selecting the Lipids under my protein.
Is it necessary to use the "update" command?
And is my assumption right that the update command only updates the nonbonded properties (Which would make no sense when there is no crystal information)
Thanks a lot,