Active Region in qm/mm calculation

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helloworld
Active Region in qm/mm calculation

Hi,

Just a general query :

How is the active region interaction energy incorporated in chemshell ?

I am using orca interface for qm region. The energy difference of qm region(28 atoms) when calculated using qm-mm chemshell-orca (taking the entire system rna in a water box taking active region(1.5k atoms) also) and when calculated using only orca comes out to be very large (around 40kcal/mol). Both the calculations have same atoms in qm region. Why is this difference so large ? Can anyone explain ?

Thank you,
Shreya

tomkeal
tomkeal's picture
Active Region in qm/mm calculation

Hi Shreya,

The QM calculation created by ChemShell will contain link atoms (if any covalent bonds are broken) and a background field of point charges in the QM Hamiltonian (if electrostatic embedding is used). If your standalone ORCA calculation does not contain either of these in the input then you will see a different energy as a result - I would guess this is the most likely reason for the difference. You should be able to check your standalone input against the one generated by ChemShell as part of the QM calculation to validate it.

Best wishes,

Tom

helloworld
By background field of point

By background field of point charges,do you mean the entire MM region charges are included in the Hamiltonian or just the active region charges ? I have a QM region, then an active region (bigger than QM) and then the entire MM region.

tomkeal
tomkeal's picture
The entire MM region will be

The entire MM region will be included unless a cutoff is specified. The active region usually refers to the atoms that are allowed to relax in a geometry optimisation, while frozen atoms will still contribute background charges to the QM calculation.

Tom

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