Questions tagged [qmmm]

For questions about applying or developing QM/MM (quantum-mechanics/molecular-mechanics) hybrid models .

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12
votes
1answer
98 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
10
votes
0answers
85 views

Periodic polarizable QM/MM embedding

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
11
votes
1answer
237 views

What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?

What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them? I realize Condensed Phase chemistry is a huge field, but ...
19
votes
2answers
747 views

Does increasing Lennard-Jones cutoff means higher accuracy?

I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
4
votes
0answers
66 views

How to properly design a modeling experiment? [closed]

How can someone properly decide on an appropriate level of theory MM, QM... What are the checklists throughout the experiment (in-silico)? How to decide a proper control case/group? For example from ...
17
votes
1answer
119 views

Benchmark transition state geometries in condensed phases

I'm seeking references/benchmarks for transition state geometries of reactions in condensed phases like crystals, zeolites, or surfaces. Basically the system just needs to be considered big, yet ...
16
votes
3answers
443 views

Is there any software that is optimized specifically for QM/MM?

A lot of codes can do Quantum Mechanics/ Molecular Mechanics (QM/MM), and I am not naively asking if there is a program that can do QM/MM. What I am interested in is a program that is purely QM/MM ...
4
votes
1answer
42 views

Defining coordinates using Vector3

I am trying to implement a tether restraint in the MM region of my QM/MM calculation using pDynamo (CHARMM/ORCA interface). I need to define the origin as a Vector3. Does anyone know how to do this?
10
votes
1answer
70 views

Constraining a set of atoms in the MM region using pDynamo (CHARMM/ORCA interface)

I am trying to perform a QM/MM optimization in which my substrate is in the MM region. However when this happens there are significant changes to the geometry (undesired). I want to avoid fixing all ...
12
votes
1answer
73 views

Q-Chem QM/MM options

I am trying to setup QM/MM calculations with QChem using user-defined connectivity and MM parameters. But the official manual is not detailed about some options. Mostly I am interested in the ...
7
votes
1answer
53 views

How to localize orbitals in pDynamo (CHARMM/ORCA interface)?

Does anyone know how to localize orbitals in pDynamo (CHARMM/ORCA interface). I am trying to identify the correct orbitals to swap for my high-spin iron(IV) system.
9
votes
1answer
75 views

How to swap orbitals in ORCA?

I am trying to swap orbitals for a high-spin iron(IV) complex. The orbitals that correspond to the iron are not in any of the SOMOs. I am using the pDynamo QM/MM program, which is an interface for ...