14 votes
Accepted

How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

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 ...
  • 1,351
13 votes

Does increasing Lennard-Jones cutoff means higher accuracy?

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 ...
  • 1,788
12 votes
Accepted

Does increasing Lennard-Jones cutoff means higher accuracy?

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_{\...
  • 15.1k
11 votes

Protein cavities - methodological starting point for basic characterization

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 ...
  • 19.2k
10 votes
Accepted

Get fractional coordinates from special Wyckoff positions

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: ...
  • 19.2k
8 votes
Accepted

What does the Neighbor command do in LAMMPS?

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 ...
  • 1,788
8 votes

What are the steps to prepare a surface for molecular adsorption simulations on it?

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 ...
  • 856
7 votes

Can the NCI (noncovalent interaction) index be generated starting with psi4?

If you call wfn.compute_hessian(), Psi4 tries to compute the nuclear Hessian which is indeed not implemented for most methods. Calling ...
  • 15.1k
7 votes
Accepted

Can the NCI (noncovalent interaction) index be generated starting with psi4?

Not a full answer of an alternative program, but just collecting the conclusions from the comments along with some additional suggestions. It appears that ...
  • 14.3k
7 votes

Which equation makes it possible to calculate the forces of attraction between a surface and molecules?

The long-range (non-chemical) interaction between a neutral molecule and a surface is dominated by van der Waals interactions. The simplest model you could use for this is a Lennard-Jones potential, ...
7 votes
Accepted

Rule-of-thumb for Morse potential cutoff in molecular dynamics?

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 ...
6 votes

How to calculate the energy of a surface?

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{...
  • 1,294
6 votes

Which equation makes it possible to calculate the forces of attraction between a surface and molecules?

The Schrödinger (or relativistic Dirac) equation is what essentially determine the interaction, and there are many free and open source programs that can perform such calculations; a recent listing ...
  • 15.1k
5 votes
Accepted

Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

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 ...
4 votes
Accepted

What are the more efficient, or easier, methods of handling electromagnetic interactions?

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 ...
4 votes
Accepted

Fermi level change in surfaces with adsorbed molecules

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 ...
  • 4,382

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