- 89
- 223 630
LAMMPS Tube
เข้าร่วมเมื่อ 25 ก.ย. 2019
LAMMPS Tube is a leading online learning platform that helps anyone learn molecular dynamics simulations and the LAMMPS package to achieve scientific goals. This platform was released by Dr. Roozbeh Sabetvand in 2018. This platform allows members to access the educational library of engaging, top-quality courses taught by recognized industry experts. For 5 years, LAMMPSTube.com has helped students and researchers in molecular dynamics simulations. With tutorials in the English language, LAMMPSTube.com is a global platform for molecular dynamics, atomic modeling, and lammps package.
Repetition of Atomic Structure with Packmol Software
Packmol is a computational software tool designed to create initial configurations for molecular dynamics simulations by efficiently packing molecules within defined spatial regions. This capability is particularly useful when simulating systems that require a specific arrangement of atoms or molecules, such as polymers or complex molecular structures in various shapes and simulation boxes.
learn more: lammpstube.com/
learn more: lammpstube.com/
มุมมอง: 28
วีดีโอ
Boron Nitride (BN) Nanotube Atomic Modeling with VMD Software
มุมมอง 6816 ชั่วโมงที่ผ่านมา
The "Nanotube Modeler" is a plugin in the VMD (Visual Molecular Dynamics) software that allows users to generate the boron nitride nanotube structure. It provides a user-friendly interface and a range of features that enable researchers to study the properties and behavior of this important nanostructure. learn more: lammpstube.com
Install and Running LAMMPS (2024 version) on Windows
มุมมอง 16014 วันที่ผ่านมา
One can follow the below steps to install LAMMPS software (2024 version) on Windows: Step 1: Download LAMMPS software from lammps.org/. Step 2: Locate and double-click the lammps.exe file. (It will usually be in your Downloads folder.) Step 3: An installation menu will appear. Bottom "install" key to install the LAMMPS package. Step 4: The software will be installed. One can now open the applic...
Vacancy Defect in LAMMPS
มุมมอง 913ปีที่แล้ว
The "delete atoms" command in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is used to remove atoms from the simulation. It allows you to selectively delete atoms based on specific criteria or conditions. Between various styles of this command, the "random" style can be used to vacancy defects defining inside the ideal structure. learn more: lammpstube.com/
Water Atomic Modeling with VMD
มุมมอง 971ปีที่แล้ว
The "Solvent Builder" module in VMD (Visual Molecular Dynamics) software is a tool that allows users to generate water boxes for molecular dynamics simulations. It simplifies the process of adding solvent molecules, such as water, around a solute molecule or system. Technically, the below steps should be followed for atomic modeling of the water box using the "Solvent Builder" module: Step 1: L...
LAMMPS Uninstallation in Windows
มุมมอง 884ปีที่แล้ว
To uninstall LAMMPS from Windows, double-click the uninstall icon in the main LAMMPS folder. With this process, removing the LAMMPS package and all its related files will begin. learn more: lammpstube.com/
Dump File (Graphical Output) in LAMMPS
มุมมอง 896ปีที่แล้ว
Graphical output in the LAMMPS package can be saved using the "dump" command in various time steps. After the dump file is produced via the LAMMPS input script, this file can be imported to other packages such as OVITO and VMD to visualize molecular dynamics simulations. learn more: lammpstube.com
Force Field Settings in LAMMPS
มุมมอง 844ปีที่แล้ว
The obtained results from the molecular dynamics simulations depend on the choice of the interatomic force field. To get correct results, we should choose the interatomic force field based on the atomic structure of the system and the physical properties under study. In this video, we described the force field setting procedure in the LAMMPS script file. learn more: lammpstube.com/
Nanotube Modeling in Avogadro Software
มุมมอง 444ปีที่แล้ว
The Nanotube Builder is a tool in Avogadro software that allows users to create and manipulate nanotube structures. It provides a user-friendly interface and a range of features that enable researchers to study the atomic arrangement of these important materials. learn more: lammpstube.com
Write Data File in LAMMPS
มุมมอง 1.1Kปีที่แล้ว
The "write_datafile" command in LAMMPS package is used to output the configuration of a molecular dynamics simulation to a data file. The data file contains information about the simulation box, atom types, masses, and coordinates, and can be used as input for subsequent simulations or analysis. learn more: lammpstube.com
Install and Running LAMMPS (2023 version) on Windows
มุมมอง 9Kปีที่แล้ว
One can follow the below steps to install LAMMPS software (2023 version) on Windows: Step 1: Download LAMMPS software from lammps.org/. Step 2: Locate and double-click the lammps.exe file. (It will usually be in your Downloads folder.) Step 3: An installation menu will appear. Bottom "install" key to install the LAMMPS package. Step 4: The software will be installed. One can now open the applic...
VolMap Outputs in VMD Software
มุมมอง 574ปีที่แล้ว
The "volmap" in VMD (Visual Molecular Dynamics) software is used to generate volumetric maps from molecular dynamics simulations or other volumetric data sources. These maps can be visualized and analyzed to gain insights into scalar properties associated with the modeled atomic system. learn more: lammpstube.com
Read 2 Data Files in LAMMPS
มุมมอง 723ปีที่แล้ว
The "read_data" command is a LAMMPS input command that reads in the initial configuration of a molecular dynamics simulation from one or numerous data files. Technically, the data file contains information about the simulation box, atom types, masses, and coordinates. learn more: lammpstube.com
Build Supercell in Avogadro Software
มุมมอง 332ปีที่แล้ว
The Supercell Builder is a tool in Avogadro software that allows users to create and manipulate large-scale atomic structures. It enables the generation of supercells, which are replicas of the unit cell that contain multiple unit cells of a material. learn more: lammpstube.com
Nanotube and Nanosheet Modeling in VMD Software
มุมมอง 760ปีที่แล้ว
The "Nanotube Modeler" is a plugin in the VMD (Visual Molecular Dynamics) software that allows users to generate various nanotube and nanosheet structures. It provides a user-friendly interface and a range of features that enable researchers to study the properties and behavior of these important nanostructures. learn more: lammpstube.com
LAMMPS Data File Create in OVITO Software
มุมมอง 2Kปีที่แล้ว
LAMMPS Data File Create in OVITO Software
Center of Mass (COM) Calculation in LAMMPS
มุมมอง 801ปีที่แล้ว
Center of Mass (COM) Calculation in LAMMPS
Radial Distribution Function (RDF) Calculation in LAMMPS
มุมมอง 3.6Kปีที่แล้ว
Radial Distribution Function (RDF) Calculation in LAMMPS
Mean Squared Displacement (MSD) Calculation in LAMMPS
มุมมอง 4.1Kปีที่แล้ว
Mean Squared Displacement (MSD) Calculation in LAMMPS
Write LAMMPS Data File with Openbabel Software
มุมมอง 2.1K2 ปีที่แล้ว
Write LAMMPS Data File with Openbabel Software
Atomic Modeling of Polymers with Avogadro Software
มุมมอง 3.4K2 ปีที่แล้ว
Atomic Modeling of Polymers with Avogadro Software
Install and Running LAMMPS (2022 version) on Windows
มุมมอง 16K2 ปีที่แล้ว
Install and Running LAMMPS (2022 version) on Windows
Very Nice Video
Cool. Any recommendation on which force field would be best to use with a BN tube like that?
Nice. Thanks for the video.
Please, how do I install the dipole package on lammps, thank you 🙏.
Please help me for script Young’s modulus and hardness
it shows 'Imp' is not recognized as an internal or external command, operable program or batch file. how to solve this
멋진 실행.
Pleae help i try to run my input file and the terminal crashes
what is the code for the dimer file?
How did you get the input script on your desktop?
if u have windows 11 or 64bit and cant open the app, go to files tab (on the download page) > avogadro2 > download the 64win one instead
Excellent!
Is there a code that does this automatically via the tk console?
I have installed new version but the old version I can’t uninstall 😢
0.000000 0.000000 xlo xhi 0.000000 0.000000 ylo yhi 0.000000 0.000000 zlo zhi why ?
In old versions of VMD software (like VMD 1.9.2) the size of simulation box prints incorrectly and must be corrected manually.
thank you
Good luck!!!
Hello, I am struggling with atom types of same element atoms which I need to denote differently in the Lammps data file from VMD. For example , in my pdb file there are 2 carbon atoms from two molecules, i dont want both of them to denoted by same atom type( say 1) in the lammps data file. Could you suggest how to solve the issue?
Jazmyne Divide
98585 Verner Canyon
Thank you so much kind sir. Love from India.
Good luck!!!
How many core-hours did this simulation take?
eu achei que eu saberia baixar um programa sozinha, mas incrivelmente tava dando erro, só seguir o vídeo que resolveu tudo, muito obrigada!
;)
Can you please put a link to download the input script . i cant find it in "examples"
🎉
;)
When creating a .data file from OVITO in atom full style , how do I add the bond, angle, dihedral and improper information?
this script?
I was trying to install lammps on ubuntu 8 feb 2023 version I am using atom style full it gives atom style full is part MOLECULE package which is not enable though I gave command make yes-all after doing make mpi , please help
Thanks :) It works for kappa calculations
You're welcome!
sir when i calculated rdf by lammps the peak for some atoms are very high especially for those atoms which concentration is low, sir how i could decrease the peak value. thank you so much sir
Clear and simple, it worked for me, thanks!
You're welcome!
how to create semiconductors like Si and GaAs. please help
lol thank u so much. i wish this software just had a graphical user interface
Hi, thank you very much! But it's flat. How can I have a 3d representation?
Hello, What are the differences of running rammps on between Windows and Linux (Ubuntu etc.)? what is the better one?
can you tell in which unit we get the surface area?
Hello,can you tell me where did the input script got created? I can't seem to find it
I can't find the input script
Hello, you can find numerous scripts in the "examples" folder of the installed LAMMPS package.
I can’t seem to find the folder for test run. May I know where can I find it?
Required lammps input script for 1-pyrenebutyric acid using PCFF forcefield I have forcefield parameter file
Great tutorial. Thank you.
You are welcome!
Why is it saying missing required information when i do same things
Please use 1.9.2 version of VMD software and follow this instructional video
@@lammpstube thank you it worked
The paper uses harominc expressions using (1/2)K, whereas the LAMMPS manual states that K already includes the traditional 1/2 factor... shoudn't the K values in the script (bond_coef and angle_coef) be divided by 2 relative to those listed in the paper? Cheers!
This paper used the DREIDING force field for various interaction parameters as below link: pubs.acs.org/doi/10.1021/j100389a010 In the DREIDING force field, the implemented formalism for bonded interaction is 1/2k(r-r0)^2 which k parameter set to 700 for each single bond. So, in the LAMMPS script, this coefficient should be set to 350 as shown in the video.
@@lammpstubeThanks for the reply. But at 02:53 the form column of the paper defines the bonding term as (1/2)Kb(r-r0)², with Kb=350.0. In the data file, the bond_coeff is 350.0 also, but in the lammps documentation shown at 02:24, the form of the bonding term is K(r-r0)². My doubt is that looking at these two expressions, shouln't K(LAMMPS) = (1/2)Kb?
In this paper, the bonding interaction formula corresponding to the chosen coefficient not reported correctly. In order to confirm my previous comment, read the DREIDING reference mentioned in the paper.
@@lammpstube I see. Thanks!
@Philipplus Good luck!
Thank you for this clarification...I was wondering how to make LAMMPS with mpi on Windows....Please help me out
This video will be released soon on the channel.
thank you very much@@lammpstube
hope this massage will find you in good health, i am facing problem related to RDF, i am simulating epoxy resin model using lammps, my system consists of C,N,O,H, i want to find out inter atomic distance between C---C, N--C, C---H using rdf, but distance which i get from rdf are larger than the inter atomic distance, my force field is oplass force field, i also try rerun method but still the problem is not solved any help will make my lifesave. thank you your sincerely Abid
Hi! This problem can be caused by various MD simulation settings. But, improper atomic modeling of epoxy or improper choice of force field can be one of the most important cases.
thank you so much for your reply i solve the problem it is due to special bond, but is it possible to added atoms in vmd, please let me know thanks@@lammpstube
Hey, thank you very much, this video was very helpful. One question is whether this procedure was to create a single biomolecule, how can I put 100 molecules in a box of water, for example?
For this, first a molecule is modeled and then it is repeated as many times as desired in a simulation box using the Packmol software. This video will be released soon on the channel.
In last of the video When i try to Run they give me this error " 'Imp' is not recognized as an internal or external command, operable program or batch file." how to fix it please help me out
As shown in the video, you need to go to the "bin" folder and make sure that you write the name of the LAMMPS executable correctly in the "cmd".
hello, which free software are good for generating lammps data file (i am working on polymer composite ) , thank you so much
Hello The following list of software can be suitable for you: A. Free Atomic Modeling Packages - Avogadro: Atomic modeling for Polymer Chains - Packmol: Repeat Chains in Defined Box - Ovito or VMD: Convert Format of Prepared Atomic Structures to LAMMPS Format (atom_style full) B. Non-Free Atomic Modeling Packages - Materials Studio - Quantum ATK
extremely well explained! thanks a lot!!!
You are welcome!
عالی💎
You're welcome!
عالی💎
You're welcome!
دکتر 💯💯
You're welcome!
How to calculate elemental MSD in a binary compound? e.g. if its NaCl, how to calculate MSD of Na in NaCl and Ca in NaCl?
For this, you must define Cl and Na atoms as separate groups, and for each group, define a separate MSD calculation command. Finally, these calculation outputs can be called in the "thermo_style" command.
@@lammpstube thank you so much.
you're welcome@@anjalishankar
Why don't i able to run it in the command prompt though i am following as it is??
Please locate your graphical output on your desktop and repeat the introduced technical steps