AMBER Archive (2008)

Subject: RE: RE: AMBER: about QMMM output

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Sat Jul 05 2008 - 21:25:47 CDT

Thank you very much for your answer!

Best Regards,
Lin
        

======= 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
>> http://amber.scripps.edu/tutorials/advanced/tutorial2/section4.htm
>> 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
>interactions.
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Assistant Research Professor |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu