Questions tagged [lammps]

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

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7
votes
1answer
115 views

Considerations when developing ab initio based interatomic potentials for classical molecular dynamics

I know that there are published interatomic potentials provided for most elements when using classical molecular dynamics tools such as LAMMPS. However, if someone were to use their own DFT ...
4
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0answers
17 views

Define stress-strain for a multi-wall carbon nanotubes bundle

I want to simulate a MWCNT bundle in which the central MWCNT is pulled out of the bundle. How to define the stress/strain curve of such system? I am building my system with scikit-nano and using ...
4
votes
0answers
11 views

Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS?

I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different ...
5
votes
1answer
42 views

Heating and Quenching simulation in lammps

I am trying to perform heating and quenching simulations of iron from various temperatures. I took 2000 atom simulation box and performed following methodology ...
6
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0answers
47 views

LAMMPS fix print function

First of all, I'm very new to LAMMPS so I'm sorry if my question is trivial. I'm trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-...
4
votes
1answer
84 views

VMD polymer draws multiple bonds

I'm new to VMD and I'm having some problems with displaying my polymer chain. Instead of just one bond, VMD draws multiple bonds. Why does this happen? I'm creating the data with Lammps, below you can ...
29
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2answers
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 ...
5
votes
3answers
175 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 ...
6
votes
1answer
83 views

How to fix "bad timestep" error in LAMMPS?

I'm working on this project where I have to simulate a gold nanoparticle impact in a gold plate, my script is: ...
6
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0answers
74 views

How do you Select a Time Step for Molecular Dynamics Simulations?

It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
5
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0answers
67 views

Apparent conservation of potential energy in NPT simulation?

I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
3
votes
0answers
50 views

Generate doped solid using LAMMPS? [closed]

Starting from a $\ce{BaTiO3}$ structure, I want to dope this with Strontium to obtain $\ce{Ba_{0.67}Sr_{0.33}TiO3}$. Is there a way to do this using LAMMPS? I began a discussion about this in Chinese ...
6
votes
1answer
47 views

KSpace style for hybrid/overlay table and dipole?

I'm trying to run lammps for a system subject to a custom short-range potential, that I have in a table, as well as the lammps lj/cut/dipole/long interaction (with LJ epsilon set to 0 because I do not ...
2
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0answers
44 views

Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
8
votes
1answer
70 views

LAMMPS input card in an NVIDIA GPU

I want to simulate the attached model for a Cu NP in Ar using my GPU, but I got erratic results. All looks well when I simulate it in my CPU with the command: ...
9
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0answers
65 views

Molecular dynamics with surfaces [closed]

I want to run molecular dynamics with LAMMPS, the aim is to simulate a platinum surface with a gas phase consisting of simple molecules. I would like to use periodic boundary conditions in order to ...
8
votes
1answer
119 views

Where to get Tersoff and SW potentials for LAMMPS

I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
3
votes
0answers
118 views

Practical way to reduce pressure fluctuations in molecular dynamics? [closed]

I am running a test setup in LAMMPS. I am using $4000$ atom hcp system with MEAM potential. The system need to be at equilibrium at $\pu{10K}$ and for this I am giving initial velocity at $\pu{10K}$ ...
14
votes
1answer
230 views

Creating Interatomic Potential for Lammps using DFT

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
13
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2answers
102 views

Best protocol for finding liquid–solid coexistence curve in molecular dynamics?

I am trying to determine the melting temperature of an fcc metal as a function of pressure, which should give a liquid–solid phase diagram for this metal. For now, I'm not going to consider any ...
7
votes
3answers
194 views

LAMMPS data files, making atom IDs contiguous

I sometimes need to remove atoms from LAMMPS datafiles by hand, removing each row that corresponds to an atomID I want to remove, then decrementing the total atom count. This causes the atom IDs to no ...
6
votes
0answers
73 views

What will be the cohesive energy of an alloy in LAMMPS? [closed]

The cohesive energy of a pure material is generally termed as the energy of a unit cell divided by the number of atoms. what will be cohesive energy of an alloy in LAMMPS? I am running LAMMPS for $\ce{...
4
votes
1answer
113 views

Calculating Velocity autocorrelation function for Binary Diffusion Coefficient

I have been attempting for some time to evaluate the binary Diffusion coefficient of argon in a gas mixture with neon. From the literature, this property can be measured using the velocity ...
7
votes
1answer
124 views

Using LAMMPS for a small system

I want to run a classical molecular dynamics simulation on silicane using LAMMPS. Since I don't have access to any HPC nor do I have a powerful desktop PC, I'm planning on making the system small. By ...
5
votes
0answers
126 views

Cannot import both numpy and LAMMPS to python after installing with conda [closed]

I installed the module LAMMPS by using this command conda install -c conda-forge lammps I want to import LAMMPS to python code, but it says: ...
11
votes
1answer
421 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 ...
10
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0answers
81 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? [closed]

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 ...
11
votes
1answer
63 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 ...
7
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0answers
43 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 ...
17
votes
1answer
185 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 ...
8
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0answers
137 views

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

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. ...
8
votes
2answers
294 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
190 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
161 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 ...
8
votes
1answer
177 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 $1 \,\mathrm{atm}$...
9
votes
1answer
519 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 ...
11
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0answers
119 views

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

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
654 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 ...
10
votes
1answer
288 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
votes
0answers
174 views

Sample LAMMPS file for graphene growth on a metal surface [closed]

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 ...
9
votes
1answer
156 views

How can I calculate the Poisson ratio of an amorphous material with LAMMPS?

I noticed that we can calculate the Poisson ratio of a crystalline metals with LAMMPS. I wonder if we can use that example for a metallic glass! If no, is there any other way, with another software?
6
votes
0answers
75 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
139 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. ...
12
votes
0answers
148 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 ...
11
votes
0answers
417 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 ...
15
votes
1answer
2k 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 ...
14
votes
3answers
569 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
486 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 ...
15
votes
1answer
161 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 ...
17
votes
3answers
266 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?