13

I am afraid I can't be of much help regarding the QM part of your simulation, but I can give some thoughts on the MM part. In short: you should use the cutoff that was used to validate your force field. While a proper ab initio method is expected to improve with a longer cutoff, this is not necessarily true for force fields. The reason for that is that force ...


13

The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here: The main issue are the units. The input parameters for reax force fields are given in "real" units by default. Unless they are converted real units have to be used in the lammps input file. Setting the units appropriately ...


11

The identification of cavities, for drug design, is beyond the geometric characterization (aka volume). The server and individual software, beside the geometrical cavity determination, characterize them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors,...


11

Very interesting question! The LJ potential is quite benign in that it has a $r^{-6}$ decay, which is pretty rapid. However, MD codes typically go a bit farther than a straightaway truncation at $r_{\rm max}$, but instead also apply an analytical correction for the region $[r_{\rm max},\infty)$. The analytical correction for the cut-off can be justified by ...


9

From that reference, what we got is the bond length from the atomic positions. One easy way is to look for a CIF file with the crystal information. From the CIF49801 bellow, we get the following info: (label type_symbol symmetry_multiplicity Wyckoff_symbol fract_x fract_y fract_z B_iso_or_equiv occupancy) Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 . 1. S1 ...


8

I'll try to outline an approach in plane-wave DFT. The main idea is to build up the system step-wise and reuse previous results as the number of atoms and therefore the computational burden will grow quickly. Lets start with the simulation using a bulk material with $N$ atoms and assume the surface direction is orientated facing the z-axis. Make sure this ...


7

Neighbour lists are not just a feature of LAMMPS, but of just about any MD engine out there. When you are evaluating your energy function, it is extremely common to have some sort of cutoff for the short-range forces, so that you reduce the complexity of their evaluation from e.g. $O(N^2)$ to $O(N)$. However, simply checking whether two atoms are within a ...


7

Since you are referring to "the Morse potential", I assume you mean to use it for modeling van der Waals interactions? If not, please ignore this answer and consider updating your question to include what kind of potential you are modeling using the Morse potential. If so, here is my answer: There is a rule of thumb based on experience and a lot of ...


6

For calculating the energy of a surface, we need to split the contribution of the surface and the contribution of the bulk to the total energy. $$E_\mathrm{total} = E_\mathrm{surface} + E_\mathrm{bulk}$$ The term $E_\mathrm{total}$ is obtained from a calculation on a simulation cell that models the surface (let this be Calculation 1). The term $E_\mathrm{...


5

You may be able to find some bounds on performance such as O(n3) based on the number of water molecules etc, but honestly benchmarks not performed on your own hardware are always somewhat hard to use or accept. Things such as memory speed can also influence things quite significantly so benchmarks are hard to look at for quantifiable differences. That being ...


4

You could simplify long range interaction by reducing precision with range. Useful algorithm for it is: https://en.wikipedia.org/wiki/Barnes%E2%80%93Hut_simulation It is usually used for gravity, but it can be applied for other forces too. With it you can do something better than just to ignore long range interaction, as is usually done, especially important ...


4

The work function is surface-dependent, and sensitive to surface reconstructions and passivation, amongst other things. The Fermi level of the infinite bulk material would be a rather crude proxy for the workfunction. You also need to be aware that the Fermi level as computed in most periodic DFT codes is calculated with respect to an arbitrary ...


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