Dear List,
I have position restraints in my system. I am keeping the interface surface
fixed whereas the protein in water is allowed to be flexible. I am planning
to perform aMD and would like to know if I should consider potential energy
with restraints or without restraints in order to calculate EthreshP?
Should I consider all atoms of the system (including fixed surface) in the
calculation or should I only take into account atoms consisting of
protein+water?
Thank you,
Regards,
Neha
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 01 2016 - 15:00:02 PDT
