You are a hero. Thanks for making these videos! I am a new PhD student working on molecular modeling. I am the first person in my lab doing this. So the only help I can get is from people like you! Thanks so much!
I am happy that I have seen this video. I don't know anything about simulation. I have been hooked, couldn't complete my project because of this, but you have shown me the way today. Thank you so much. I still want you to enlighten me more. Your English is clear enough. I'm Eche Emmanuel Sylvester. From Nigeria.
Input file can be written in notepad++, atom softwares etc. For creating input model, you can also use lammps. Adding to this, Their are lots of software available which can build the input structure for you( packmol, avogadro,Material studio etc)
I don't have experience with MD but 4.58 at line 9 seems more suitable for a liquid than for a gas. However thank you fot the video. it is really usefull.
In the lammps documentation there are three arguments for pair_coeff for the same lj/cut pair style instead of two, what does this third argument signify?
very helpful video, thanks! I have a question, you trigger the molecular using "velocity" command. Can I just use "fix 1 all NPT temp xx xx 100 iso 1 1 100 " instead? What's the difference? Thank you for any suggestion !
You can't do that way... In MD simulation you need to provide initial velocity to the system which is only done through velocity command. And About nvt, npt and nph: These commands perform time integration on Nose-Hoover style non-Hamiltonian equations of motion which are designed to generate positions and velocities sampled from the canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This updates the position and velocity for atoms in the group each timestep.
Certainly! You provided an input file for a single atom. Could you now provide input files for molecules such as water or CO2? Additionally, if possible, include examples for polymers like PMMA and PA. @@Vinay192
@@jagadeeshwarreddy9597 You can create your model using packmol and then use vmd to generate input file for lammps. If you are not aware of this method, I will post a video on this.
@@sayanchatterjee8399 You can write the code in a simple text editor. You can run with "lmp -in input.in". lmp is executable here which could be same or different for ur case.
@@VIKASHKUMARSINGH-bo2qx Right now I have only experience of working with lammps and as far I know it could be used...the important thing is to have the right interaction potential for your material..
Thank you so much sir. It is really helps me a lot. Can you please tell be concept of compute comment in lammps. I want to calculate charge of each atom in my system (NVE) in ReaxFF, for each time step (from beginning to end). Some people said use fix qeq/reax comment in input file. I tried this but I don't know where I have to get the output (charge of each atom for each time step). Can you please help me sir
Great video ! thank you. I am PHD biomecanics student and i am working on micro indentation with AFM on humain cells. Can you please do and indentation exeple ? GOOD LUCK !
Sir, i am trying to simulate sodium acetate trihydrate.. And see its properties in different temperatures. Currently I have made a dat file. What atom style should I use. I am stuck here. Any help would be useful. Thanks Adhish
You are a hero. Thanks for making these videos! I am a new PhD student working on molecular modeling. I am the first person in my lab doing this. So the only help I can get is from people like you! Thanks so much!
Good luck champ👍
I'm also a first year PhD student. And I'm also the first person using LAMMPS in my lab. And I found this tutorial very helpful as well.
@@rafidbendimerad Thanks Rafid...Good Luck!
2nd year Mtech first one doing MD LAMMPS
Hello
We are the same situation. I'm too a new PhD student. Do you have email?
I have some equations for you.
I am happy that I have seen this video. I don't know anything about simulation. I have been hooked, couldn't complete my project because of this, but you have shown me the way today. Thank you so much. I still want you to enlighten me more. Your English is clear enough. I'm Eche Emmanuel Sylvester. From Nigeria.
Very well explained. Looking forward to see more such videos including some more physics involved in the system.
very good tutorial keep going sir...
🙏
Thanks for the video. Insightful!
Thank you very much for this video sir! Excellent and concise.
Crystal clear expression Vinay sir! Keep posting video on LAMMPS, It will be very helpful
Thanks Somesh....Will upload more soon..
Many thank it was very interesting
Excellent explanation.
Great tutorial thankyou sir. can you tell me which software you using to create input file sir.
Input file can be written in notepad++, atom softwares etc. For creating input model, you can also use lammps. Adding to this, Their are lots of software available which can build the input structure for you( packmol, avogadro,Material studio etc)
please create more videos about lammps simulations. u have nice videos
Thanks for your encouraging words... Definitely I will create more videos on lammps...
I don't have experience with MD but 4.58 at line 9 seems more suitable for a liquid than for a gas. However thank you fot the video. it is really usefull.
thanks for explaining it so well, i have a question ,after writing the input script ,how can i run it in cmd ? also what text aditor is this ?
@@adnankhattak6899"lmp -in input.in"
lmp is executable (check what is the name of executable in your case). Text editor is "Atom".
In the lammps documentation there are three arguments for pair_coeff for the same lj/cut pair style instead of two, what does this third argument signify?
It is unit of energy. You can go through this video to understand it well: th-cam.com/video/milojYy5soI/w-d-xo.html
very helpful video, thanks! I have a question, you trigger the molecular using "velocity" command. Can I just use "fix 1 all NPT temp xx xx 100 iso 1 1 100 " instead? What's the difference? Thank you for any suggestion !
You can't do that way... In MD simulation you need to provide initial velocity to the system which is only done through velocity command.
And About nvt, npt and nph:
These commands perform time integration on Nose-Hoover style non-Hamiltonian equations of motion which are designed to generate positions and velocities sampled from the canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This updates the position and velocity for atoms in the group each timestep.
@@Vinay192 thank you so much for the explain! I'll try this right away.
Very well explained. Can you make a video on polymers as well?
Can you elaborate a bit?
Certainly! You provided an input file for a single atom. Could you now provide input files for molecules such as water or CO2? Additionally, if possible, include examples for polymers like PMMA and PA. @@Vinay192
@@jagadeeshwarreddy9597 You can create your model using packmol and then use vmd to generate input file for lammps. If you are not aware of this method, I will post a video on this.
Yeah, bruh, I'm not aware of this. Could you please do a video on that and post it? @@Vinay192
Great Video! I am with difficult with extension save the data file. Could You help me with this?
Yes. Save your input script in notepad with xyz.in extension.
Where to write the coes for LAMMPS? And how do you execute the files to get the result? Can you elaborate on these points? Thank you.
@@sayanchatterjee8399 You can write the code in a simple text editor. You can run with "lmp -in input.in". lmp is executable here which could be same or different for ur case.
What software we can use to construct complex molecule and how to create their data file?
Like what?
@@Vinay192 I have to make tobermorite?
@@VIKASHKUMARSINGH-bo2qx Right now I have only experience of working with lammps and as far I know it could be used...the important thing is to have the right interaction potential for your material..
great explanation
keep going!!!!we are back up you!
Thanks a lot..🙏
Hi, how to relax the structure and record the energy after relaxation?
Thanks, sir for this video please tell the command to increase the pressure on the system?
With fix command, you can vary pressure in the system.
Hi Curie'X, Please i will like you to please help me get this right. AFter writing on input script/file, how do you upload it on lammps to run?
You don't have to upload anywhere. Just run in the terminal using the " lmp_serial -in input.in" on the window local machine.
Is there any way to print the potential energy of a group in a text/dat file?
Thank you so much sir. It is really helps me a lot. Can you please tell be concept of compute comment in lammps. I want to calculate charge of each atom in my system (NVE) in ReaxFF, for each time step (from beginning to end). Some people said use fix qeq/reax comment in input file. I tried this but I don't know where I have to get the output (charge of each atom for each time step). Can you please help me sir
Unfortunately, never tried this.....
May be it can help(Not sure): docs.lammps.org/fix_qeq.html
@@Vinay192 thank you sir
@@hingiesmonisha3038 let me know if you able to do..
@@Vinay192 sure sir.
@@Vinay192 successfully got the charge of each atom sir. Thank you sir
Please make more videos taking some examples of liquids also
can you help me with my script? i got stuck at verlet run
Thank you sir...❤️❤️❤️
Great video ! thank you. I am PHD biomecanics student and i am working on micro indentation with AFM on humain cells. Can you please do and indentation exeple ? GOOD LUCK !
Do you have input files to run SPC/FQ water model in LAMMPS
Hi, can you show me with an example how to calculate thermal conductivity in a metal (for example) by applying heat in one segment ? many thanks
Bro I want to create a slab of Cu(100). Please help
It should not be that much complicated
Hi, Can you please explain how to create molecules (like H2O, CH4, Ethanol, etc) from the create_atoms command? Thank you
Could you please tell me if you have some ideas on this question?
Thanks for the video..but please make a video how to run the lammps file in commamd prompt
Please watch the previous video..I have explained there.
@@Vinay192 can you give the link here please?
@@mezbahahmed6506 th-cam.com/video/idgZ7zc7jQI/w-d-xo.html
I wrote input scripts in vi editor ,how to run this in linux ,can anyone tell me ?
I need your help in my work on lammps
How to create ellipsoid region in lammps
Unfortunately, I never tried this. Please share if you get any idea how to do it.
Hello, thank you for you're video, it was really helpful. Could you please explain how to do a simulation of water (H2O) molecules please? Thank you
Very Helpful! Thanks
Thanks bro🙏
i have a problem with addforce command, can you help me?
do well to provide link to script
Sir, i am trying to simulate sodium acetate trihydrate.. And see its properties in different temperatures. Currently I have made a dat file. What atom style should I use. I am stuck here. Any help would be useful.
Thanks
Adhish
Till now I have only worked with metals and gases and used atom style which stores position and velocity of atoms with time evolution...
Thank you
Sir how to create hollow atoms(having outer and inner radius) in simulation box
May I know which project you are working upon?
@@Vinay192 kishansidh786@gmail.com plz drop a mail
@@Vinay192 computational study of mechanical properties of hollow nanoparticles
Helpful thanks
Pleasure
NIce
Thanks bro ❤️
i want to take online class i will pay fess
👍