AMBER Archive (2008)

Subject: RE: RE: AMBER: about QMMM output

From: linfu (
Date: Sat Jul 05 2008 - 21:25:47 CDT

Thank you very much for your answer!

Best Regards,

======= 2008-07-05 03:55:10 您在来信中写道:=======

>Hi Linfu,
>> Thank you very much for profs. Ross and Gustavo's answer.
>> >Note that E(QM/MM)VDW is
>> >calculated classically and so this gets included in the general VDWaals
>> >energy term.
>> However, from tutorial
>> the result below shows
>> when NSTEP =0, in my opinion, sander hasn't started doing MD and just
>> calculated energy(?)
>> at this time VDWAALS should be the same for Classical and QM/MM method,
>> However,
>> they differ much in VDWAALS term (VDWAALS=930.8446 in classical and
>> VDWAALS=881.6951 in QM/MM)
>Ah, but you are forgetting that classically VDW includes the
>MMligand-MMligand interaction but when you run a QM/MM calculation there is
>no QM-QM VDW term since that is implicit in the calculation of ESCF (and
>unfortunately can't really be decomposed from that). Hence what you see for
>VDW when you run the QM/MM calculation is the sum of MM-MM and QM-MM VDW
>terms. QM-QM terms are zero. From your example above you can conclude that
>the difference 49.1495 Kcal/mol is from what would have been QM-QM VDW
>All the best
>|\oss Walker
>| Assistant Research Professor |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
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