Questions tagged [forcefields]

Questions related to forcefield development and use in matter modeling.

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11
votes
0answers
65 views

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 ...
6
votes
1answer
50 views

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 ...
10
votes
2answers
389 views

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 ...
7
votes
1answer
83 views

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 ...
6
votes
1answer
87 views

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 ...
10
votes
1answer
160 views

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, ...
7
votes
1answer
47 views

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 ...
3
votes
1answer
33 views

Missing residues in ATB downloaded pdb/rtp files

I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md) Two files are available: a PDB file and a topology ITP/RTP file. The name of the ...
11
votes
2answers
61 views

What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?

I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
6
votes
2answers
96 views

Symmetry-preserving low-level structural relaxation

I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
14
votes
2answers
153 views

Finding parameters for a molecule in various forcefields

Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...
9
votes
3answers
387 views

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...
15
votes
1answer
83 views

Which modelling package currently implements an AI derived force field?

I would like to use an AI-derived force field as they seemed to have lesser computational cost. Which simulation package (Gromacs, Amber, NAMD...) currently implement some of them?
8
votes
1answer
55 views

Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
9
votes
1answer
59 views

What is the state-of-the-art in current flexible water models?

Do we have water models so far which are flexible? How good can they model specific properties of water and are they currently used with force fields and in actual simulations?
6
votes
0answers
96 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
23
votes
1answer
140 views

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
6
votes
0answers
63 views

How do I generate an aluminum force-field for a LAMMPS input file? [closed]

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
17
votes
2answers
2k views

What is the cutting edge for open-source Force-Field generation?

The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions ...
14
votes
0answers
85 views

Generating interatomic potentials via force matching [closed]

I am trying to learn best practices for force matching ab initio molecular dynamics (AIMD) data with nonlinear least-squares minimization to generate interatomic potentials for use in classical MD. I ...
22
votes
1answer
190 views

Benchmarking data for Ewald summation algorithms

Are there good benchmarks available for testing homemade Ewald summation code? Optimally it would be very nice if there was several types of systems. NIST has a very nice benchmark for energies of ...
31
votes
2answers
354 views

Machine learning interatomic potentials for molecular dynamic simulations: are they good?

I know the general question of machine learning in computational chemistry has been already raised here: What is the current status of machine learning applied to materials or molecular systems? ...
13
votes
2answers
226 views

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

This is a doubt regarding the usage of various forcefields together in MD simulation of hydrates. For Eg., we use TIP4P/ice for water molecules, OPLS-UA for methane and EPM2 for carbon dioxide and so ...