Questions tagged [lammps]

For questions about (or related to) the software LAMMPS.

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10
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0answers
62 views

Using Molecular Dynamics as an experimentalist to study how much plastic work is converted to heat, does anyone have any comments on our paper?

When you load a metal and the deformation results in permanent plastic deformation, the input work should be converted into heat and thus dissipate. But for about 100 years people have struggled to ...
12
votes
1answer
54 views

Modelling nitrogen interstitial barrier to oxygen diffusion in metals

I want to study the effect of nitrogen interstitials on oxygen diffusion in metals and vice-versa. Would you suggest MSD calculations in LAMMPS to be a viable method for this? There aren't many ...
8
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0answers
38 views

Reaction simulation at specific temperature, pH and pressure [closed]

Can we design metal organic frameworks, layered double hydroxide using LAMMPS? How? I want to synthesize a metal organic framework or such materials, and I want to ask if I put two to three chemicals ...
11
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0answers
91 views

Empirically determining thermostat damping factor

tl;dr Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? I am computing a set of simulations in LAMMPS, using ReaxFF, ...
5
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0answers
71 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
9
votes
2answers
124 views

Tools for structural analysis on LAMMPS trajectories

I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
11
votes
1answer
107 views

How does one compute the boiling point of a liquid made of a particular molecule?

This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE. I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
9
votes
2answers
121 views

How to build a simulation model for a molecular dynamics simulation

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
9
votes
1answer
100 views

Modelling water using the TIP3P flexible system [closed]

I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
8
votes
1answer
133 views

Using the VACF command in LAMMPS to get the velocity autocorrelation function

I am writing a simple Lennard-Jones fluid simulation in LAMMPS. So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
12
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0answers
75 views

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
11
votes
1answer
144 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 ...
11
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1answer
90 views

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
12
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0answers
82 views

Sample LAMMPS file for graphene growth on a metal surface

I am working with graphene growth on metal substrates. But I need some sample files to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
7
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0answers
55 views

How do I generate an aluminum force-field for a LAMMPS input file? [closed]

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
20
votes
1answer
122 views

Why can't I reproduce the behavior of an H-saturated graphene flake?

I'm trying to simulate a graphene flake with its edge C atoms saturated by H atoms, in a temperature ramp from 300 K to 1600 K, using LAMMPS and the AIREBO potential proposed by Stuart et al. in 2000. ...
13
votes
0answers
82 views

Poiseuille flow by LAMMPS [closed]

I am trying to model 3D Poiseuille flow of an argon gas confined between two parallel platinum plates by using LAMMPS. I have one reference paper, as given in [1] below. I built my platinum structure ...
12
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0answers
164 views

How to convert a molecular structure made in Avogadro to a LAMMPS coordinate file? [closed]

I was trying to convert a crystal structure into a LAMMPS data file in Avogadro but whenever I type .lmpdat as an extension, it says "The file name is not valid". Can you tell me any ...
12
votes
1answer
668 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
3answers
506 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
18
votes
1answer
285 views

How to optimize zinc oxide bulk structure at certain pressure with LAMMPS

I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS. However, I approached a problem that the fluctuating ...
16
votes
1answer
152 views

Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?

I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
16
votes
3answers
119 views

Does anyone know any software for MD simulation which include the effect of magnetic field?

I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?