How to Prepare Input Files & Run Any Liquid Simulation with LAMMPS/GROMACS using OPLS force field
ฝัง
- เผยแพร่เมื่อ 25 ก.ย. 2024
- Welcome to Molecular Mindset! This tutorial explores how to effortlessly generate data files for LAMMPS, GROMACS, and many other engines that perform molecular dynamics simulations.
💻 Learn how to generate files in minutes, customize parameters, and visualize molecular structures.
🛠️ Follow our step-by-step guide to set up the environment, and generate molecular simulation force fields using the SMILES string of your molecule of interest.
Stay tuned for an exciting challenge! 🏆 Participate for a chance to win exclusive prizes, including discounts on our upcoming Masterclass. Comment your responses below and join us in mastering advanced molecular dynamics simulations! 💡
-- LINKS --
Blog:
molecularminds...
Downloading and Installing Lammps and VMD
• How to install LAMMPS ...
GitHub Repository:
github.com/Mol...
Molecular Simulation Design Framework (MoSDeF) :
mosdef.org/
Follow us of X:
/ molecmindset
Don't forget to subscribe, leave feedback, and explore more fascinating content with us. See you in the next video! 🔬✨
#Tutorials #StepbyStep #InstallationGuide #Guides #Linux #Chemistry #MachineLearning #Physics #ComputationalScience #ScientificSoftware #HowTo#OpenSource #Dynamics #ComputationalChemistry #MolecularDynamics #Compchem #biochemistry #ScienceEducation #SimulationSoftware #ResearchTools #UbuntuTutorial #LinuxTips #STEM #LearnLAMMPS #GROMACS
Touluene: avg. density = 0.016 g/cm^3 && error in density = 98.177%
Probably did something very wrong :/
I did everything the same except creating a sample_outputs/ directory to store the results
Error could be with the equil.inp file; what is the overlap=0.2 ?
Also I'm unable to view the dcd files using: mol load dcd etho_npt.dcd
Would you be releasing the solutions on your github repo?
Touluene avg. density = 0.826 && error in density = 4.618%
P.S. I converted the num = round() function to math.floor() function