Questions tagged [molecular-interactions]

Questions related to molecular interactions when calculating quantities in materials science.

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19
votes
2answers
631 views

Does increasing Lennard-Jones cutoff means higher accuracy?

I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
9
votes
1answer
135 views

Get fractional coordinates from special Wyckoff positions

I'm trying to get the fractional coordinates for Mo and S, for MoS$_2$-2H, where 2H means the phase. MoS$_2$-2H is a bilayer, in which each layer is separated from each other by Van der Waals forces. ...
10
votes
1answer
46 views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
12
votes
1answer
408 views

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

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
12
votes
1answer
50 views

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

Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
6
votes
1answer
54 views

How to calculate the energy of a surface?

I want to study the interaction of a surface with some molecules (green house effect gases). To obtain the binding energy, the procedure is to calculate the energy of both systems separately $E_\...
12
votes
1answer
123 views

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

I want to study the interaction of a given surface with some molecules. How should I prepare the surface for that kind of simulation? By prepare the surface I mean how many atom layers, how many of ...
15
votes
1answer
61 views

Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
17
votes
1answer
101 views

Fermi level change in surfaces with adsorbed molecules

In a DFT standard calculation of a solid 3D material (i.e. bulk metal), one of the properties that can be obtained is the Fermi level $E_F$. This feature is related with the required work to add an ...