Molecular Dynamics Simulations Complete Part 3

Molecular dynamics simulations complete part 3 --- This time we enter the last discussion on molecular dynamics simulations (my version) hehe, namely on QM / MM. Why do I call this last discussion? Well because this discussion is the last chapter of the few references in the lab AIC. I have not found references about simulation MC, AIMD, BOMD etc. in the lab. so I ends meet a series of molecular dynamics simulations to here alone ..

This article will only cover about QM / MM is often done in the lab AIC, although QMCF (Quantum Mechanic Charge Field) also includes QM / MM, but because it looks like a dissertation from Pak Poncho is being borrowed and not returned, then it will not be dealt with on QMCF here , Why should QMCF? I understand to accommodate simulation 3+ ion with a charge up that can not be handled by the QM / MM usual well (well, just as I recall hell).

The basic idea of ​​the QM / MM is very simple, MM can be applied to large systems but less accuracy, while QM has better accuracy but can not be used for large systems with millions of atoms. Therefore, the idea of ​​how important a part they want to learn treated with QM methods while its bulk system is treated with MM. Departing from here, we can limit the system to be treated by QM, eg for ion solvation in water or ammonia, only the first solvation shell or second shell (if you have sufficient computers) that were treated with QM, while the solvent system itself is treated with MM. To adjust the distance to be treated with QM (first solvation shell) could be based on ion distribution function with N from classical molecular dynamics simulation results. Style system can be written as:

Where Fsistem style MM of the total system, FMK is style MK (quantum mechanics) in the region MK and FMK / mm is the molecular mechanics force within the MK. So that the particles can move from region to MM QM will require a smoothing function.

2 smoothingpersamaan function.

Illustration QM / MM can be illustrated in the figure below.

qm-mmgambar 1.

Okay, I think it is quite got here discussion of molecular dynamics simulations that have been gained from lectures, discussions with friends in the lab AIC. Some references that I use are as follows:

# Armunanto, R., 2004, Simulation of Ag +, Au +, Co2 + in Water, Liquid Ammonia and Water-Ammonia

Mixture, Dissertation, Leopold-Franzens-Universität Innsbruck, Austria.

# Urip, 2009, MOLECULAR DYNAMICS SIMULATION scandium (I) IN LIQUID AMMONIA METHOD AB INITIO QUANTUM MECHANICS / MECHANICS MOLECULAR, thesis, University of Gadjah Mada, Yogyakarta.

# Sukir, 2011, MOLECULAR DYNAMICS SIMULATION HYBRID QUANTUM MECHANICS / MECHANICS MOLECULAR Y2 + ION IN LIQUID AMMONIA AND WATER.

# Some good book for learning the molecular dynamics simulations

# Daan Frenkel, Berend Smit, 2002, Understanding Molecular Simulation, ACADEMIC PRESS, USA.

#Akira Satoh, 2011, Introduction to Practice of Molecular Molecular Dynamics Simulation, Monte Carlo, Brownian Dynamics, Lattice Boltzmann, Dissipative Particle Dynamics, Elsevier, japan.

and one paper that discusses the following methods of molecular dynamics simulations modern.

# Smit, B., 2008, Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity, Chem.Rev, 108, 4125-4184.

Okay, enough of and hopefully...see you!