# Tag Info

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

Many published papers, even extremely highly cited ones by what you call "serious" authors, have issues like these. Consider for example this one which currently has 862 Google Scholar ...
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### Is the DYNAMO code developed by LAMMPS still available?

This is Steve Plimpton. So far as I know there is no official DYNAMO website or download location. The code long pre-dates the popularity of source code "repositories". It was developed by Daw and ...

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

I was actually going to provide this as a comment as this in itself is not a proper answer. But since this got a bit too lengthy for a comment, I am providing this as an answer. It is possible for a ...
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### Is the DYNAMO code developed by LAMMPS still available?

There is a page on the Sandia labs website that includes download links for all the software developed by Steve Plimpton. It sounds as if he reimplemented all the functionality of DYNAMO into a ...
• 13.9k
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### 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 ...
• 1,341
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### How does one compute the boiling point of a liquid made of a particular molecule?

I would like to start off by saying this is first and foremost a thermodynamic problem. Secondly, and as a result of thermodynamics, refer to Gibbs Phase Rule which says F = C - P + 2 ...
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### 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 ...
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### Using LAMMPS for a small system

There are a couple of potential problems. First, the assumption of periodic simulations is that your box size is large enough that there is no effect on an atom from its nearest periodic replica. I ...
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### How to fix "bad timestep" error in LAMMPS?

Your problem comes from the line: fix 11 A print v_com "coords of center of mass" file cdm.dat As per the documentation, the correct syntax is:...

### How to make input script file for nanoparticle using LAMMPS?

You can either use python or MATLAB to generate the coordinates, or even use the built in tools in LAMMPS. To do this in LAMMPS, you only need to follow three steps. Use the lattice command to define ...
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### What are some open-source codes that can generate potentials?

My answer is based on Lammps Creating interatomic-potential which predicts every property of different phase is a nightmare job. There are few database which is already available for inter-atomic ...
• 3,054
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### Empirically determining thermostat damping factor

To the best of my knowledge, there is no universal or even near-universal heuristic for what the time constant should be. The only rule of thumb I have encountered is that the time constant should be ...

### Tools for structural analysis on LAMMPS trajectories

You can use OVITO as well which allows you to post-process your dump file https://www.ovito.org/
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### How to make input script file for nanoparticle using LAMMPS?

Atomsk You can use this software to play with the structure and then, generate de coordinate file for you program. Atomsk is a free, Open Source command-line program dedicated to the creation, ...
• 18.5k
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### Considerations when developing ab initio based interatomic potentials for classical molecular dynamics

There is quite abit of work going on in this field right now. Take a look at what Rogers et al. are doing using MP2 to derive all aspects of a force-field. They are also working on a DFT ...
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### Selection of appropriate Langevin damping parameter for MD of solid metal

I know it's a boring thing to say, but: It depends on what you want to do. The way I use Langevin thermostats, is to ensure good equipartitioning in my setup, so that I don't have any local hotspots ...
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### Best protocol for finding liquid–solid coexistence curve in molecular dynamics?

I'm not an expert in this area, but I think there are currently several approaches to this, none of them undisputed. Maybe this recent paper that tests a few of those methods will provide some ideas/...
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### Does anyone know any software for MD simulation which include the effect of magnetic field?

I think that there isn't one. As the cause of the magnetic properties are the electrons, and no MD codes consider the electrons, they are unable to simulate magnetism.
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