how to ensure molecules adopt their favor orientations in SMD simulation

From: crazylyf (crazylyf_at_163.com)
Date: Tue Apr 06 2010 - 22:39:11 CDT

Hi everyone,
I am running a SMD simulation and I want move a target molecule through a membrane protein, but I don't know how to ensure the molecule adopt its favor orientations during the simulation. If I apply a force on an atom which isn't at the exact molecular center, does this affect the simulation? If yes, how can I optimize the simulation?
Best regards,
Crick

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