AMBER Archive (2008)

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

From: Fan Yanping (chefy_at_nus.edu.sg)
Date: Tue Oct 07 2008 - 01:08:14 CDT

Dear Amber community
 
I try to calculate the binding energy by mm_gbsa,here's the result
 
ELE               -8.21       7.60
VDW              -20.20       2.07
INT               -4.72       1.09
GAS              -33.14       7.93
GBSUR             -3.08       0.16
GB                10.08       5.45
GBSOL              7.00       5.40
GBELE              1.86       4.77
GBTOT            -26.14       5.06

In 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).

Could any body point me out how to modify my simulation to make INT close to 0.Thanks

Yanping

 
 
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