MedeA-VASP includes a comprehensive graphical interface to set up, run and analyze VASP calculations. 1 (I am currently using my own multiply patched version 5. In solid-state physics, the electronic band structure (or simply band structure) of a solid describes the range of energies that. Vienna Ab-Initio Simulation Package VASP visualization VASP GUI Visualize Visualization View Viewer DOWNLOAD vaspGUI 0.04 PreAlpha / 0.03 for Windows Load comments. 5.8 CONTCAR file Up: 5 Files used by Previous: 5.6 IBZKPT file. 5.7 POSCAR file This file contains the lattice geometry and the ionic positions, optionally also starting velocities and predictor-corrector coordinates for a MD-run.
Requests for technical support from the VASP group should be posted in the VASP-forum.
- 2Input
- 3Calculation
Task
In this example the nucleophile substitution of a Cl- by another Cl- in CH3Cl is simulated using bluemoon sampling.
Input
POSCAR
In the blue moon sampling method several POSCAR files are used for different values of the collective variable.
KPOINTS
- For isolated atoms and molecules interactions between periodic images are negligible (in sufficiently large cells) hence no Brillouin zone sampling is necessary.
INCAR
- The setting LBLUEOUT=.TRUE. tells VASP to write out the information needed for the computation of free energies.
Calculation
In the blue moon method, the free energy difference is computed by integration of the free energy gradients computed for several points differing in the value of the collective variable distributed between known inital and final states. The gradients for each point are computed within a constrained molecular dynamics simulation (note the value of STATUS=0 for the collective variable defined in the ICONST file).
Running the calculation
The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD (note that the free energy is independent of the masses of atoms). The simulation for each of the points along the reaction coordinate is performed in a separate directory called 1, 2, ..., 7. These are created automatically by the run script. For practical reasons, we split our (presumably long) blue moon calculation into shorter runs of length of 1000 fs (NSW=1000; POTIM=1). This is done automatically in the script run which looks as follows:
Free-energy profile
The free energy gradient is obtained as a ratio of two averages (see Constrained molecular dynamics). This is done by the script fgradBM.sh, which writes the free energy gradient vs. the collective variable to the file grad.dat:
To execute that script type:
For our purposes, a simple trapezoidal rule can be used for the integration of gradients. For accurate calculations, more sohpisticated integration schemes should be considered.The free energy vs. collective variable is obtained by forward integration using the script integrateForward.py:
To execute that script type and write to the file free_energy.dat:
Finally to plot that file type:
The free energy profile should look like the following:
Note that much longer simulations should be performed (typically a few tens or hundreds of ps) in order to achieve well converged averages needed in accurate calculations.
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Abstract: Aquation free energy profiles of neutral cisplatin and cationicmonofunctional derivatives, including triaminochloroplatinum(II) andcis-diammine(pyridine)chloroplatinum(II), were computed using state of the artthermodynamic integration, for which temperature and solvent were accounted forexplicitly using density functional theory based canonical molecular dynamics(DFT-MD). For all the systems the 'inverse-hydration' where the metal centeracts as an acceptor of hydrogen bond has been observed. This has motivated toconsider the inversely bonded solvent molecule in the definition of thereaction coordinate required to initiate the constrained DFT-MD trajectories.We found that there exists little difference in free enthalpies of activations,such that these platinum-based anticancer drugs are likely to behave the sameway in aqueous media. Detailed analysis of the microsolvation structure of thesquare-planar complexes, along with the key steps of the aquation mechanism arediscussed.
Submission history
From: Lionel Truflandier [view email][v1]Tue, 3 Mar 2020 10:07:52 UTC (5,157 KB)
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