Questions tagged [charmm]
Questions about the molecular simulation program CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM primarily targets biological systems including peptides and proteins, but also finds broad applications for inorganic materials with applications in materials design.
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CHARMM36 Parameters for Neutral Arginine
I am looking for CHARMM36 parameters for Neutral Arginine. Protonated form of Argnine is already available in CHARMM36 library, but not the same for Neutral. Thanks.
With best regards
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4
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MMGBSA: Electrostatic and van der Waals
I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
- 41
8
votes
2
answers
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Silica (α-cristobalite) water system generation
I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
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Creating Amber/CHARMM style force field potential for energetic materials using DFT [duplicate]
What are the basic steps and methodologies used in creating inter-atomic force field potential for CHARMM/Amber style for energetic materials with the help of DFT? What are the best possible free ...
2
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0
answers
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CHARMM-gui creates empty space between LPS-s and terminates while building e. coli outer membrane with peptides above it [closed]
I'm trying to build outer membrane of e. coli with small peptides above it, with CHARMM-GUI. Peptides should be positioned above the membrane, but CHARMM-GUI creates space for them between LPS (...
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8
votes
1
answer
485
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Alternative to CGenFF for generating large ligand topology
I am now preparing a ligand topology following GROMACS protein-ligand tutorial.
However, I have a large ligand (446 atoms).
$ wc -l my_ligand.pdb
446 my_ligand.pdb
...
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Lone pairs in CHARMM for molecular dynamics [closed]
I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file:
...
- 1,526
4
votes
1
answer
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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?
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10
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1
answer
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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 ...
- 1,526
7
votes
1
answer
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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.
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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 ...
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