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 ...
Fabian's user avatar
  • 1,411
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 ...
Godzilla's user avatar
  • 1,918
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_{\...
Susi Lehtola's user avatar
  • 19.1k
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 ...
Camps's user avatar
  • 23.3k
11 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: ...
Camps's user avatar
  • 23.3k
9 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 ...
CKl's user avatar
  • 876
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 ...
Godzilla's user avatar
  • 1,918
8 votes

Silica (α-cristobalite) water system generation

Proper Way If you have access to CHARMM program, you can try writing a patch to passivate the dangling silicon atoms with OH groups. But if you decide to go this way, please be advised that you must ...
Hemanth Haridas's user avatar
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 ...
Susi Lehtola's user avatar
  • 19.1k
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 ...
Tyberius's user avatar
  • 15.5k
7 votes
Accepted

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, ...
Stephen's user avatar
  • 721
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 ...
patrickmelix's user avatar
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{...
Mythreyi's user avatar
  • 1,359
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 ...
Susi Lehtola's user avatar
  • 19.1k
5 votes
Accepted

Silica (α-cristobalite) water system generation

As you note, any structure with dangling silicon atoms cannot be considered correct. I'm surprised CHARMM-GUI would produce a structure with undercoordinated (<4 bonds) silicon. I can't really tell ...
WaterMolecule's user avatar
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 ...
Tristan Maxson's user avatar
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 ...
Phil Hasnip's user avatar
  • 7,157
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 ...
Surprised Seagull's user avatar
4 votes
Accepted

Can radial distribution function determine where the interactions of reference (atom/molecule) reduces greatly with surrounding atoms/molecules?

Your assumption regarding the RDF plot is generally correct. The RDF provides information about the probability of finding particles at a given distance from the reference atom/molecule. Analyzing the ...
Jaafar Mehrez's user avatar
3 votes
Accepted

What is the significance of xtb message: Interaction energies are not physical?

The error message states Interaction energies Attention: monomers are not optimized Interaction energies are not physical This suggests that the interaction energy is computed as ...
Susi Lehtola's user avatar
  • 19.1k
2 votes

Non-Covalent Interaction between drug and DNA?

Since it has been a month since OP agreed to write an answer without actually writing the answer, I will try answering this. The easiest way is to perform something called Enhanced Sampling ...
Hemanth Haridas's user avatar
2 votes

Adsorption of naphthalene on graphene oxide sheets with gmx

There are a couple of strategies that I know of in the literature. The first one is the so-called chemical vapour deposition. It is fairly easy to script, you can find details on the procedure in this ...
Anon's user avatar
  • 161
2 votes

How to calculate ionic radius in Gaussian?

Does it really need to be done in Gaussian? I found a paper(1) titled "Atomic and Ionic Radii of Elements 1-96" where they calculated it for a large fraction of the periodic table: Abstract:...
ksousa's user avatar
  • 4,108
2 votes

PSI4 SAPT calculation: failure to write

I suspect it turned out to be an issue with scratch space. I moved the scratch location to a local compute node instead of a networked filesystem scratch space. The variable to be set up is $...
bhopshang's user avatar
  • 233
2 votes

VASP with VDW dispersion corrections for a large system

It was killed, this indicates something externally killed it. Likely a manager for the cluster preventing you from running long jobs on the front end or the job simply ran out of time. Simply submit ...
Tristan Maxson's user avatar
1 vote

Adsorption of naphthalene on graphene oxide sheets with gmx

The set-up for the MD simulation depends on what you want to observe or what quantities you want to compute. If you want to set-up the MD simulation of the adsorption of a single Naphthalene molecule ...
Roshan Shrestha's user avatar
1 vote

References for Electrostatics Calculations Used in Molecular Dynamics

The reason why most molecular force fields stop at point charges and dipoles is they're good enough. What we mean by "good enough" is for the electrostatic potential (ESP) around a classical ...
Shern Ren Tee's user avatar

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