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Questions tagged [molecular-interactions]

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

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20 votes
2 answers
1k 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 ...
mykd's user avatar
  • 2,342
16 votes
1 answer
6k 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 ...
SaiSmaran S B PES1201701189PES's user avatar
13 votes
1 answer
177 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 ...
Camps's user avatar
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12 votes
1 answer
251 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?
anneb101's user avatar
  • 995
7 votes
2 answers
195 views

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

Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation? [Clarification 1] Between a ...
SFriendly's user avatar
  • 967