exercises:2015_pitt:aimd
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exercises:2015_pitt:aimd [2015/03/03 09:37] – [AIMD of water] vondele | exercises:2015_pitt:aimd [2015/03/03 11:58] – vondele | ||
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====== AIMD of water ====== | ====== AIMD of water ====== | ||
- | < | + | < |
Topics: | Topics: | ||
* MD section (timestep) | * MD section (timestep) | ||
* Thermostat (NVE, NVT, NPT) | * Thermostat (NVE, NVT, NPT) | ||
+ | |||
+ | ===== 1st task: prepapre inputs for MD ===== | ||
Start from the '' | Start from the '' | ||
Line 114: | Line 116: | ||
+ | ====== Analysis ====== | ||
+ | |||
+ | While running the MD simulations, | ||
+ | |||
+ | ===== 2nd task: visualize the .ener file ===== | ||
+ | |||
+ | A first quick check can be performed using the file '' | ||
+ | < | ||
+ | # Step Nr. Time[fs] | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | This can be easily visualized with gnuplot, for example for the conserved quantity (plotting the second vs the sixth column) : | ||
+ | < | ||
+ | gnuplot> plot ' | ||
+ | </ | ||
+ | |||
+ | To judge if this is actually well conserved, compare to the potential energy: | ||
+ | < | ||
+ | gnuplot> plot ' | ||
+ | gnuplot> replot ' | ||
+ | </ | ||
+ | |||
+ | If the constant of motion is not well conserved, try to | ||
+ | * Make '' | ||
+ | * Make '' | ||
+ | * Play with '' | ||
+ | |||
+ | To judge if a system is well equilibrated is not easy. At least the temperature and the potential energy of the system must oscillate around an average and be free of long term drift. As a rule of thumb, discard 1/3 of the trajectory, use 2/3 for data analysis. | ||
+ | |||
+ | ===== 3rd task: visualize/ | ||
+ | |||
+ | We will use vmd to analyze the trajectory file. Note that the generated trajectory is only a few 100s of fs, typically, 10s of ps are needed for even for basic properties. | ||
+ | |||
+ | Start vmd | ||
+ | |||
+ | < | ||
+ | vmd WATER-pos-1.xyz | ||
+ | </ | ||
+ | |||
+ | ==== g(r) ==== | ||
+ | |||
+ | In the menu go to : | ||
+ | |||
+ | Extensions/ | ||
+ | Utilities/ | ||
+ | |||
+ | 1st, set the unit cell as needed. Now improve the Graphics/ | ||
+ | |||
+ | 2nd, compute the O-O pair distribution function (Selections='' | ||
+ | |||
+ | How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? | ||
+ | |||
+ | === IR spectrum === | ||
+ | |||
+ | Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, | ||
+ | |||
+ | Create the following file | ||
+ | <code - charges.dat> | ||
+ | O -1.2 | ||
+ | H +0.6 | ||
+ | </ | ||
+ | |||
+ | Go to Extensions/ | ||
+ | Select the proper molecule (WATER-pos-1.xyz), | ||
+ | Utilities/ | ||
+ | Compute spectrum. | ||
+ | |||
+ | Where do you expect the OH stretch to be ? Is this reproduced ? | ||
+ | |||
+ | < | ||
+ | |||
+ | ===== 4th task: simple ions in solution ===== | ||
+ | |||
+ | < | ||
+ | |||
+ | Introduce an ion in your system, and equilibrate this system. Study its dynamics and solvation structure. | ||
+ | |||
+ | The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, | ||
+ | Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp> | ||
====== Required files ====== | ====== Required files ====== |
exercises/2015_pitt/aimd.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1