Questions tagged [qmmm]

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

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3 votes
1 answer
94 views

How to model TS for given a small biomolecular system?

In this paper (e.g. doi:10.1021/cs500093h and other applied QM/MM studies), it is demonstrated several transition states, intermediates, and products of given set of biomolecules (several residues, ...
  • 181
4 votes
0 answers
51 views

Periodic boundary conditions or spherical potential? [closed]

I was wondering whether you know if there is any sort of literature discussing whether periodic boundary conditions or spherical potentials could be better or worse for QM/MM or MM simulations, their ...
3 votes
1 answer
74 views

Calculate the atomic charge for transition metal using RESP?

I calculate the atomic charge using restricted electrostatic potential (RESP) and compute with the Hartree Fock method. This method is OK for organic compounds, but for complexes that contain ...
8 votes
1 answer
122 views

Parameterize a complex that contains Transition metal (Build Force Field)?

It is a general question. I know, but I need some help. I am interested to parametrize a complex that contains transition metal like Ru and Pt etc. Furthermore, I will use this Force Field to do ...
12 votes
1 answer
121 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 ...
  • 1,982
12 votes
0 answers
119 views

Periodic polarizable QM/MM embedding [closed]

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 ...
  • 1,982
12 votes
1 answer
251 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
2 answers
899 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 ...
  • 1,982
4 votes
0 answers
67 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 ...
  • 1,311
17 votes
1 answer
122 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 ...
  • 7,794
16 votes
3 answers
678 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 ...
  • 4,066
4 votes
1 answer
44 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?
  • 1,496
10 votes
1 answer
81 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 ...
  • 1,496
12 votes
1 answer
80 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
1 answer
73 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.
  • 1,496
9 votes
1 answer
111 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 ...
  • 1,496