2024 Winter Molecular Simulation Seminar

How we run the simulation?



It is easy to run a simulation, but much more difficult to understand the underlying principle.

We will ask questions about simulation-related methodologies. For instance,

How the Newtonian equation of motion is actually integrated?

How can we set the temperature and pressure of given system to be constant?

What differences and similarities do the force field models have?

What can be computed using MD simulation and how can we bring physical insights?

Why do we sometimes use MC and sometimes MD?

Can we model polarizability and reactivity in classical molecular simulation?

Can we trust the simulation result?

...



We strive to answer these questions and try to understand how molecular simulations actually work.

Schedule

Event TypeDateDescriptionMaterials
Week1 - How MD works?
Seminar 1 1/12
(Fri)		 Integration Algorithm
- Stability (Symplecticity)
- Efficiency (Constraint/HMR/MTS)
- Accuracy (Configurational/Dynamics) 		[abstract]
[material]
Seminar 2 1/12
(Fri)		 Classical Force Field Model
- Water/Ion Force Field
- Biomolecular Force Field
- Ionic liquid Force Field 		[abstract]
[material]
Seminar 3 1/12
(Fri)		 Force and Energy Computation
- Lennard Jones and Electrostatics
- How PME becomes dominant?
- GPU parallelization 		[abstract]
[material]
Week2 - How to sample ensembles?
Seminar 4 1/26
(Fri)		 Constant Ensemble Simulation
- Thermostatting algorithm
- Velocity-rescaling algorithm
- Artifact on using thermostat 		[abstract]
[material]
Seminar 5 1/26
(Fri)		 Monte Carlo
- NVT, NPT, muVT ensemble
- Gibbs ensemble for phase coexistence
- Osmotic ensemble 		[abstract]
[material]
Seminar 6 1/26
(Fri)		 Enhanced Monte Carlo
- Chain molecules (Rosenbluth/CBMC)
- Condensed phases (CFCMC/NCMC)
- Accelerated MC (ECMC/Latent Space MC) 		[abstract]
[material]
Week3 - What to compute?
Seminar 7 2/24
(Thu)		 Thermodynamics - Free energy Calculation I
- Reaction coordinate
- Umbrella sampling
- Metadynamics 		[abstract]
[material]
Seminar 8 2/24
(Thu)		 Thermodynamics - Free energy Calculation II
- Enhanced Sampling
- Nonergodicity
- Choice of CV 		[abstract]
[material]
Seminar 9 2/24
(Thu)		 Kinetics - Rare event Simulation
- Early approches (TST/Bennet-Chandler)
- Markov chain Monte Carlo (TPS/TIS/kMC)
- Splitting (FFS/Milestoning) 		[abstract]
[material]
Seminar 10 2/24
(Thu)		 Special - Markov State Model
- Markvoian Process
- Markov State Model
- Simulation with MSM 		[abstract]
[material]
Week4 - How to extend the scope?
Seminar 11 3/29
(Fri)		 Coarse-Grained Simulation
- Coarse-Graining
- MARTINI
- Future of CG 		[abstract]
Seminar 12 3/29
(Fri)		 Polarizable Simulation
- Drude oscillator
- Induced Dipole model
- Charge equalization 		[abstract]
Seminar 13 3/29
(Fri)		 Reactive Simulation - Polymerization
- Bond breaking
- In Situ Polymerization 		[abstract]
Seminar 14 3/29
(Fri)		 Reactive Simulation - Proton Transport
- Constant pH simulation
 [abstract]

Facilitators

  • Seonghyun Kang

    Force and Energy computation, Monte Carlo, Thermodynamics - Free energy Calculation I, Polarizable Simulation

  • Sangmin Lee

    Integration Algorithm, Enhanced Monte Carlo, Kinetics - Rare event Simulation, Reactive Simulation - Proton & Electron Transport

  • Seungbin Hong

    Classical Force Field, Constant Ensemble Simulation, Thermodynamics - Free energy Calculation II, Coarse-Grained Simulation

  • Kyeongjun Jeong

    Reactive Simulation - Polymerization

  • Junho Lim

    Thermodynamics - Markov State Model

Contact

Please contact us if you have any questions or queries about our seminar.
smlee99 [at] postech [dot] ac [dot] kr