[AMBER] sander QM/MM MD

From: Masoud Kazemi <kazemimsoud.gmail.com>
Date: Wed, 20 Jul 2016 14:26:50 +0200

I am using AMBER 12 to do QMMM calculation using G09 as external QM
package. I have a couple questions and I would be grateful
if somebody could help.

   - 1) Is it electronic embedding? The user manual (Amber 12) state that "*For
   QM/MM simulations with electronic embedding it is mandatory to specify the
   charge of the** QM region in the &qmmm namelist with variable qmcharge
   in addition to specifying the charge** in the namelist that is**
   specific for the external QM program". *But I received the message that
   these keywords are deprecated (charge in the case G09)*.* The Gaussian
   input "*#P M062X/6-31g** SCF=(Conver=8) NoSymm Force Guess=Read Charge
   Prop=(Field,Read)*" contains the *charge* keyword and the coordinate/MM
   charges of the surrounding. I think this means the electrostatic part of
   environment is included in the QM Hamiltonian and the calculation is EE. I
   would be grateful if somebody could confirm this.
   - 2) How *EXTERNESCF* is realated to SCF in G09? I am also confused
   about the sander output. For a point in my calculation I get,*
   EXTERNESCF= -216070.1690* while the G09 output for same point is *SCF
   Done: E(RM062X) = -1704.92860364*. The G09 energies are A.U which if
   converted to kcal/mol or kj/mol would be very different from the value
   given as *EXTERNESCF. *what is this discrepancy?

Thank you for your help.

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Received on Wed Jul 20 2016 - 05:30:03 PDT
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