AMBER Archive (2008)

Subject: AMBER: internal energy INT is not zero from MM_GBSA

From: flyanping (flyanping_at_hotmail.com)
Date: Tue Oct 07 2008 - 01:18:49 CDT

Dear Amber community:I used mm_gbsa to calculat binding free energies,however the final result showed:ELE -8.21 7.60VDW -20.20 2.07INT -4.72 1.09GAS -33.14 7.93GBSUR -3.08 0.16GB 10.08 5.45GBSOL 7.00 5.40GBELE 1.86 4.77GBTOT -26.14 5.06In the tutorial ,it's said the INT = internal energy arising from bond, angle and dihedral terms in the MM force field. (this term always amounts to zero in the single trajectory approach).Mine is not 0,what does INT=non zero mean? How it happened ?Anything wrong with my calcs?Could any body point me out how to modify my simulation to make INT close to 0.
Thanks&regards,Yanping
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