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--- exercises:2015_pitt:aimd [2015/03/03 10:12] – vondele
+++ exercises:2015_pitt:aimd [2015/03/03 11:58] – vondele
@@ Line 118: / Line 118: @@
 ====== Analysis ======
 While running the MD simulations, it is useful to check that all is fine. Here, we do some basic analysis, to look at the structure and dynamics of the liquid.
 ===== 2nd task: visualize the .ener file =====
@@ Line 149: / Line 149: @@
   * Play with ''EXTRAPOLATION_ORDER'' (to reduce drift and or instabilities)
-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.
+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/analyze the trajectory file =====
+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
+<code>
+vmd WATER-pos-1.xyz
+</code>
+==== g(r) ====
+In the menu go to :
+Extensions/Analysis/Radial Pair Distribution Function g(r)
+Utilities/Set unit cell size dimensions
+st, set the unit cell as needed. Now improve the Graphics/Representations to also show neighboring unit cells and visualize hydrogen bonds.
+nd, compute the O-O pair distribution function (Selections=''name O'') and similar for the O-H pair distribution function (including their integrals).
+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, namely classical point charges for the water molecules. In this context the approximation is reasonable.
+Create the following file
+<code - charges.dat>
+O -1.2
+H +0.6
+</code>
+Go to Extensions/Analysis/Spectral density calculator.
+Select the proper molecule (WATER-pos-1.xyz), adjust the timestep (0.5fs), and the maximum frequency (6000 cm^-1).
+Utilities/Load name<->charge map from file.
+Compute spectrum.
+Where do you expect the OH stretch to be ? Is this reproduced ?
+<note> Lower frequencies need longer trajectories for reasonable estimates, at the very least 10 times the period of the signal </note>
+===== 4th task: simple ions in solution =====
+<note> This task is optional, and can be performed at the end of the tutorial if time is available. </note>
+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, and must be run for a while before it is representative.
+Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp>Grotthuss_mechanism |the Grotthuss mechanism]] ?
 ====== Required files ======