> On Apr 24, 2018, at 6:09 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Tue, Apr 24, 2018, James Kress wrote:
>
>> Once I am done with the ORCA calculation, I wish to superimpose the results
>> of that calculation (i.e. surface information) on the total system (one that
>> includes both the QM and MM atoms). However, I cannot figure out how to get
>> the coordinate system of the QM calculation properly superimposed on the
>> total system. It appears the QM atoms have been relocated through some
>> geometric transformation when Amber generates the QM/MM files.
>>
>> How do I retain the original coordinates of the QM section prior to Amber
>> cutting it out of the entire system for QM/MM setup? I could find no
>> discussion about this in the manual nor in the mailing list.
>
> I'm having trouble understanding where the problem lies. Here's my view
> of how Amber handles coordinates in QM/MM:
>
> 1. You start with a structure of the whole system, maybe from xray,
> maybe from model building.
>
> 2. Set up in Amber, and indicate which atoms belong to the quantum
> region. This shouldn't change any coordinates; (use "set default
> nocenter on" if your full system is a periodic one.)
>
> 3. Amber creates an input file of just the quantum atoms (plus link
> atoms.) I think the coordinates in this file are just the ones in the full
> structure (from step 1).
>
> 4. Orca calculates forces, but doesn't modify the coordinates.
>
> These steps don't mesh well with your statement that "QM atoms have been
> relocated ...when Amber generates the QM/MM files", but I'm not sure
> exactly what you are referring to. Can you give more specifics about
> the stage where the QM atoms are getting in the "wrong" place?
Under periodic boundary conditions, the geometric center of the QM region atoms is translated to the origin of the coordinate system. This simplifies identifcation of MM atoms within the QM/MM cutoff, which are included as external point charges in a QM/MM calculation with electrostatic embedding. These translated coordinates are used in the QM calculation.
I think Jim wants to display the results from the QM calculation (such as orbitals) including the MM environment, for instance with vmd. To achieve this you have to translate back the coordinates / results from the QM calculation, or translate the MM coordinates. sander does not print the offset, so you have to calculate it yourself by comparing coordinates of e.g. the first atom in the QM region at each time step.
All the best,
Andy
> ....dac
>
>
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Received on Tue Apr 24 2018 - 22:30:02 PDT
