On 04/25/2016 03:46 AM, 王美婷 wrote:
> Dear all
> I want to calculate the free energy difference between QM/MM Hamiltonian and MM Hamiltonian for an acetamide molecule soaked in periodic boxes of TIP3P waters. For the QM/MM simulation, the QM region is the solute molecule acetamide and the MM region is water. The QM method used in the QM/MM simulation is BLYP/6-31g* .
Presumably you mean to get the relative solvation free energies? The
QM/MM to MM free energy is completely arbitrary and physically
meaningless. If you are interested (and not already aware) Koenig and
Brooks have several papers comparing the relative solvation free
energies of such methods and also have tested several ways of computing
them from pure MM trajectories.
> I use SANDER module with option imin=5 to calculate the potential energy of each step of the QM/MM MD (with the same parmtop and imaged crd )。 The input file of imin=5 and QM/MM were attached.
> My quetions are:
> 1, The potential energy of the same snapshot given by QM/MM MD (which can be read in the output file) is different to that calculated by SANDER with imin=5, the energy of QM region is almost the same, but the other items have large difference especially for the BOND term. I want to know why?
This should always be the case. The energies in sander are a (half?)step
behind the trajectory file due to the leap frog integrator.
Your only choice is to re-evaluate the trajectory within imin=5 twice.
> 2, I also want to know whether the potential energy printed in the out file of QM/MM MD is the total potential energy of the system or not? Any scale or missing terms used here ?
See above. There shouldn't be any scaling unless you are looking at QM
output in hartrees for some reason.
> 3, Is the vdW term printed in QM/MM MD out file is the sum of the vdW interaction energy among the solvent molecules and that between QM and MM region?
vdW interactions are pure MM terms in AMBER unless you use the (highly
experimental) QXD module.
> 4. Is the ELE item printed in QM/MM MD out file only include the electrostatic interaction between QM and MM region?
I believe (but am not certain) that the QM SCF energy is not included in
that total. Obviously the SCF energy includes electrostatic components.
The MM/MM electrostatics are also obviously part of the EELE term.
>
> --
>
> mt wang
>
HTH,
Brian
>
>
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--
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Mon Apr 25 2016 - 17:00:02 PDT
