exercises:2017_uzh_acpc2:l-j_flu
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exercises:2017_uzh_acpc2:l-j_flu [2017/04/08 10:57] – [Part II: Force Field Parameter] jglan | exercises:2017_uzh_acpc2:l-j_flu [2017/05/09 08:57] – [Part IV: Ensembles] jglan | ||
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distance between atoms i and j. | distance between atoms i and j. | ||
- | Periodic boundary conditions should be used in this simulation. The atom near the ”edge” | + | [[https:// |
- | of the simulation box interacts with atoms contained in the neighboring image of the box. To | + | |
- | prevent artifacts, it requires a cut-off value of rij for the L-J potential. For realistic results, the | + | |
- | cut-off should be less than the half of the simulation box size and over σ Radial distribution | + | |
function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids, | function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids, | ||
etc.), describes how density varies as a function of distance from a reference particle. | etc.), describes how density varies as a function of distance from a reference particle. | ||
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In this section, a commented CP2K input example for an MD calculation is provided. | In this section, a commented CP2K input example for an MD calculation is provided. | ||
- | Comments are added, they start with an exclamation | + | Comments are added, they start with a hash mark '#' |
=== 1. Step === | === 1. Step === | ||
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< | < | ||
*Run the calculation and visualize the trajectories using VMD | *Run the calculation and visualize the trajectories using VMD | ||
- | *Run calculations with different timesteps (0.5 2 5fs), different temperatures(84, | + | *Run calculations with different timesteps (0.5 2 5fs), different temperatures(84, |
</ | </ | ||
===== Part II: Force Field Parameter | ===== Part II: Force Field Parameter | ||
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< | < | ||
**TASK** | **TASK** | ||
- | *Plot the Lennard-Jones potential against Ar-Ar distance $r$ (2-4 Å) using different \epsilon and \sigma. | + | *Plot the Lennard-Jones potential against Ar-Ar distance $r$ (2-4 Å) using different |
*Repeat the L-J MD calculation with different $\epsilon$ and $\sigma$, and compare the potential energy, temperature evolution, and explain the relation between calculated properties and force field parameters. | *Repeat the L-J MD calculation with different $\epsilon$ and $\sigma$, and compare the potential energy, temperature evolution, and explain the relation between calculated properties and force field parameters. | ||
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Step up NPT calculation, | Step up NPT calculation, | ||
+ | & | ||
+ | ... | ||
+ | STRESS_TENSOR ANALYTICAL | ||
+ | ... | ||
+ | &END FORCE_EVAL | ||
+ | ... | ||
+ | ... | ||
&MD | &MD | ||
ENSEMBLE NPT_I #constant temperature and pressure using an isotropic cell | ENSEMBLE NPT_I #constant temperature and pressure using an isotropic cell |
exercises/2017_uzh_acpc2/l-j_flu.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1