Questions tagged [forcefields]
Questions related to forcefield development and use in matter modeling.
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What is the simplest classical force field to set up?
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 ...
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In DFT codes, which energy is forces derivatives of?
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 ...
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Forcefield parameterization techniques
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?
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Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS
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 ...
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Significant differences between NPT and NVT equilibrated simulations
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 ...
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Modelling excited states using classical MD simulations
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 ...
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How to write the REBO force field
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 ...
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Advantages/Disadvantages of Qeq over Drude polarizable model?
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 ...
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How to pre-optimize metal-organic complexes in RDKit using UFF?
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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Why are Coulomb interactions modeled with just r, not r squared?
As far as I understand (as a complete beginner to molecular simulation and modelling), Coulomb's law for two atoms i and j is:
$$F=k\frac{q_iq_j}{(r_{ij})^2}$$
(the force is proportional to the ...
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Effect of temperature on Forcefield parameters in classical molecular dynamics simulations
In classical molecular dynamics simulations of complex molecular systems, the force field (FF) contains information about bonded (bonds, angles, dihedrals and impropers) and non-bonded parameters. It ...
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Is the term "Forcefield" only reserved for MD (Molecular Dynamics)?
As far as I understand, there are two related concepts called potential and forcefield. A forcefield is essentially a sum term of more than one potential.
My question is, is the term "Forcefield&...
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Include Li+ in force field for Molecular Dynamics
I want to perform some MD including Li+ ions. Specifically I am interested in Li-TFSI (aka Lithium bis(trifluoromethanesulfonyl)imide).
I tested both the ATB repository and LigParGen and neither can ...
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Training a ML forcefield on a simple bulk material
Lately, I've become quite intrigued by the recent advances in machine learning forcefields within the field of computational chemistry. I've developed a curiosity about training a simple forcefield on ...
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What is the procedure to develop a new force field for molecular simulation?
Suppose, I want to develop a novel force field for proteins.
What is the empirical procedure I should follow to do that?
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Classical MD Simulation for mineralization process
I'm currently trying to simulate the calcium carbonate mineralization process on the surface of nanoparticles. In here, I've already borrowed the classical force-field parameters on here(https://pubs....
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When and why are torques needed in molecular dynamics simulations?
I have seen that many MD simulations compute the torques due to dipole-dipole interactions and other interactions. I understand that there is a torque on a dipole in an electric field. I don't ...
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Reference textbooks for calculating pressures/stress/strain/tensors? [closed]
Is there a good reference textbook for calculating pressures/stress/strain/tensors in materials - vapor, liquids and solids? Pure physics is fine, but it would be a bonus if it also included force-...
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Force field for charged peptide-ion system
I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
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How to Derive the Kong-Chakrabarty Mixing Rules
Background
In the world of atomistic modeling with classical force fields, one is often given a force field defined by like interactions (e.g. argon-argon interactions). If one is working with a ...
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How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?
I asked this at Biostars but the post seems to have been deleted there.
My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
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Rotational invariance of anisotropic polarization models
After writing out this question, I actually figured out the answer, but I am surprised I haven't seen this detail mentioned in almost any paper on the topic, so I will answer my own question here in ...
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What causes atoms to not interact in LAMMPS? [closed]
I am trying to set up a LAMMPS simulation for depositing graphene on a nickel substrate. I am using ReaxFF forcefield. However, the carbon atoms just pass through the nickel atoms. Can anyone help me ...
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How do I put two forcefields in the same LAMMPS code? [closed]
I need to put two interactions of ffields in the same code, but, I don't know what is the problem with the way I tried it. The code shows me ...
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Re-parametrization of force fields in LAMMPS [closed]
I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
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Attempts to define atomic energies based on electron density?
The concept of an atom in a molecule is undefined in quantum mechanics. Consequently, very useful properties like atomic charges, bond orders, and so on cannot be rigorously defined. There are many ...
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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 ...
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What does it mean by "transferable" in the case of a force field?
According to Wikipedia:
Functional forms and parameter sets have been defined by the developers of interatomic potentials and feature variable degrees of self-consistency and transferability. When ...
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What software implements UFF
I am looking for common software packages that implement UFF ideally with an example of how to run it to calculate forces and energies. I see that Rdkit should be capable of doing this for example, ...
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How can we test the force field (parameter) for a complex?
I built a force field for a complex. How can I check if the force field is working well or no?
I did a short molecular dynamics using AMBER only for the complex using the parameters I built. It worked ...
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Where to find/ to get Tersoff and Stillinger Weber Potentials for MD simulation using LAMMPS
I'm trying to calculate the thermal properties of Silicene with hydrogen and halogen atoms. My problem is that, there's seems no available potential for Tersoff and Stillinger Weber Potential. and I'...
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Gromacs generate forces using .pdb topol.top and .mdp file [closed]
Given the start configuration (.pdb), topology file (topol.top) and run file(water.mdp).
I want to generate the forces on atoms. I tried, using:
...
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Basics of numerical energy minimization techniques used in molecular dynamics?
The question below describes my plan to make a basic molecular dynamics calculation using a Python script rather than a canned, self-contained program.
There seems to be three parts:
a model of the ...
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DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?
The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
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What are the advantages of (semi)-empirical force fields over Machine Learning Potentials?
I am currently working with ReaxFF, an empirical reactive force field that can describe chemical bond forming and breaking. The main advantage over ab initio methods are of course the greatly ...
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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 ...
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Constructing a molecular polarizability tensor from sets of atomic polarizabilities?
Often empirical electrostatic models or molecular force fields approximate the molecular polarizability using an additive model, e.g., for N atoms:
$$
\alpha_{mol} = \sum_i^N \alpha_{atom_i}
$$
This ...
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Applicability of GFN-FF force field and other xTB methods for dynamics of ions in water [closed]
I am working on a project involving water clusters with ions in them. One of the problems that I ran into quite early on was that good forcefield parameters are not available for highly charged ions ...
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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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Simple code for polarizable force-field molecular dynamics? [closed]
I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple "toy repositories" for these models such as is ...
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What does "force field" mean?
In MD simulations we often hear the term force field.
What is it?
We know, for example that, Gromacs provides various types of forcefields.
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Calculate FF interaction energy of small molecular dimers [closed]
I have a set of molecular dimers (~25 atoms) for which DFT-D3 interaction energies are calculated by Psi4 and Turbomole program. Now I want to compare these values against Force-Field methods like UFF/...
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Limitations of pairwise additive forcefields
What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?
user2026
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Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?
My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...
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Where can I find/generate force-field parameters for common inorganic anions in water?
I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
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How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?
I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
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Where to get Tersoff and SW potentials for LAMMPS
I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
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Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?
I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
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Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?
I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein.
There is a particular target for which AMDock Vina, with its default force fields, ...
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How to go from Tinker parameter file to GROMACS topology file for improper and proper dihedrals?
I have been playing with a polymer called glyme, and I have run Tinker analyze on it to get OPLS-AA parameters for it. I have attached the output parameter file to this post.
My question is, how do I ...
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