Skip to main content

Questions tagged [lammps]

For questions about (or related to) the molecular dynamics software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator).

Filter by
Sorted by
Tagged with
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
16 votes
2 answers
999 views

How may I create an interatomic potential using DFT?

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
Pranav kumar's user avatar
  • 4,278
12 votes
1 answer
2k views

Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
anneb101's user avatar
  • 995
7 votes
4 answers
2k views

What are some open-source codes that can generate potentials?

can anyone give me some list recommendations of software or open source that can generate potential
deee's user avatar
  • 129
6 votes
1 answer
776 views

How can I create a small graphene flake for LAMMPS?

I've installed and can run LAMMPS on macOS as desdribed in Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output and I'm looking forward to my first Xene ...
uhoh's user avatar
  • 2,034
6 votes
3 answers
1k views

How to make input script file for nanoparticle using LAMMPS?

Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...
user4100's user avatar
31 votes
2 answers
4k views

Can a highly-cited published paper have this type of error?

Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently? Here is my problem: I have been testing a force field published ...
Barbaud Julien's user avatar
18 votes
1 answer
389 views

Empirically determining thermostat damping factor

Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
geo's user avatar
  • 455
7 votes
1 answer
1k views

Lost atoms in LAMMPS

What I am trying to simulate is an evaporation of ammonia water, after being heated by a gold plate underneath. But I have received a lost atom error during minimization. If I removed the minimization ...
Jack's user avatar
  • 71
4 votes
0 answers
71 views

Is it possible to generate a non-predefined nanotube in VMD? [closed]

I know that generating a Carbon Nanotube (CNT) in VMD, I can get the required LAMMPS input file. Since VMD makes my life way easier, giving me the position, angle and bonding information in the format ...
Delaram Nematollahi's user avatar
3 votes
0 answers
74 views

Lost atoms in a lammps simulation

I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting. ...
Kieran's user avatar
  • 763
2 votes
1 answer
319 views

Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output

I've installed presumably the latest executable version of LAMMPS for macOS from https://docs.lammps.org/Install_mac.html and tried to run the following tutorial https://github.com/mrkllntschpp/...
uhoh's user avatar
  • 2,034
0 votes
0 answers
37 views

Weird time-averaged temperature v.s. distance figure result

I am computing the thermal conductance for the structure 'Al2O3-bilayer graphene-Al2O3' along the z axis, with the following input file. ...
Kieran's user avatar
  • 763