Andy,
That's exactly the information which I needed.
Thanks to you and David.
Jim
-----Original Message-----
From: Goetz, Andreas <agoetz.sdsc.edu>
Sent: Wednesday, April 25, 2018 1:27 AM
To: David A Case <david.case.rutgers.edu>; AMBER Mailing List
<amber.ambermd.org>
Cc: James Kress <jimkress_58.kressworks.org>
Subject: Re: [AMBER] Atom position changes when setting up QM/MM calculation
> 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 Wed Apr 25 2018 - 11:30:02 PDT
