Questions tagged [forcefields]

Question 1

I have been reading a paper on the use of GNN-based methods for rapidly assigning partial charges to atoms, which becomes a type of direct chemical perception. This is particularly useful in the case ...

Question 2

Consider the following use case: I have three sets of FF parameters that are individually optimized to correspond to three different states that my system can exist in. I am trying to perform an MD ...

Question 3

My background is in the domain of classical FFs, where the terms in the potential are explicitly parameterized for bonds, angles, dihedrals and charges. Since the potential has a functional form $$ V(...

Question 4

I've been stuck at this problem for a while mostly due to lack of expertise. My main problem revolves around finding RDF and CN for molten salts with dopants. I've come to understand melting directly ...

Question 5

I have performed an on-the-fly machine learning force field (MLFF) calculation using VASP for my structure during a slow heating run from 100 K to 1200 K in the NPT ensemble for 200 ps, obtaining a ...

Question 6

I am working on a Python script to assign and detect CHARMM atom types for each atom in a molecular complex. So far, I haven't found any existing tools for this besides the CGenFF web server. My ...

Question 7

What is the simplest force field to set up? I need to generate the potential energy of some conformers of amino acids and ligands in xyz files. I am not too concerned about the force field other than ...

Question 8

There was a discussion in our research group recently, that I did not follow completely, but the crux was: In most DFT codes (especially VASP), when we compute the forces, which energy are the forces ...

Question 9

Suppose I have a novel synthetic protein. I want to find the classical forcefields that accurately models the dynamics and thermodynamics of the protein. How do I do that?

Question 10

I am working on a project that requires generating a large dataset of Co3O4 and Fe3O4 structures under various temperatures and pressures using LAMMPS. The structures will be used for training machine ...

Question 11

I am performing a set of classical MD simulations using a type of ReaxFF description to study aluminate Oligomerization. I have performed two sets of simulations, one where the system is equilibrated ...

Question 12

My question is related to the question here but not exactly the same. The studies which have looked into the excited states of molecules have generally done it by parameterizing the ground-state and ...

Question 13

I want to use the REBO-CHO force field to study graphene oxide using lammps. But I don't know how to create the input file with the parameters by reading the article or if there is a tutorial or ...

Question 14

For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach ...

Question 15

I have run into a particular problem while trying to automate my input file generation for ORCA calculations. Apparently, I either do not fully understand how SMILES strings work, or I am demanding ...

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Questions tagged [forcefields]

Construction of Graph Neural Networks to predict properties

Is it possible to smoothly interpolate between FF parameters as a function of some variable?

Derivatives of a function without an expression? Needed for calculating the force from a machine-learned potential

AIMD for DeepMD potentials and optimization with MD for AIMD

Machine learning force field prediction run verification with VASP on-the-fly MLFF feature

Assigning CHARMM Atom Types in Python Without Relying on CGenFF Web Server

What is the simplest classical force field to set up?

In DFT codes, which energy is forces derivatives of?

Forcefield parameterization techniques

Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS

Significant differences between NPT and NVT equilibrated simulations

Modelling excited states using classical MD simulations

How to write the REBO force field

Advantages/Disadvantages of Qeq over Drude polarizable model?

How to pre-optimize metal-organic complexes in RDKit using UFF?

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