Molecular Dynamics Simulation | Gromacs Installation (Win&Linux)| BeginnerTutorial | Bioinformatics

Подписаться 21 тыс.

Просмотров 103 тыс.

50% 1

In this video we will learn how to install the GROMACS in windows (steps are similar in ubuntu) and I am also going to show you a beginner tutorial of MD simulation Protein in water.
If your have error in installation or other troubleshoot issue join in our Facebook group : / 261045198486665
Instagram : / bioinformatics.bb
Molecular dynamics is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.
Minimum System Requirement
Intel Core i5 processor
16 GB RAM
1 TB hard disk
4 GB Graphic Card
MD simulations software’s: en.wikipedia.o...
Gromacs: manual.gromacs....
Gromacs Tutorial: www.mdtutorials...
CUDA installation: www.pugetsyste...
GPU installation : www.nvidia.com...
Gromacs Installation: manual.gromacs....
ions.mdp : bit.ly/3k4LbtF
mini.mdp: bit.ly/3bxIqxD
NVT.mdp: bit.ly/3i3VBJa
NPT.mdp: bit.ly/35anZWz
md.mdp: bit.ly/357XJMx

Опубликовано:

3 окт 2024

Ссылка:

Скачать:

Готовим ссылку...

Добавить в:

Мой плейлист

Посмотреть позже

Комментарии : 86

@baischoice1743 4 года назад

amazing work! Couldn't have done it without your tutorial. You broke down such a daunting task in a step by step fashion, thanks a lot!

@jaannawaz2007 3 года назад

You're very welcome!

@duc-hainguyen8499 2 года назад

@@jaannawaz2007 Dear Sir, could you help me with issue. After I run this command. gmx pdb2gmx -f modified -o 1.gro -p 1.top -water spce I have this issue: File input/output error: 1.top

@priyathiru3333 2 года назад

Thank you sir u really helped me to learn molecular dynamics and has beginner it's really helpful ❤️🔥and I nearly watched your nearly 50 to 100 times to learn step by step and part 2 simulation gromacs I nearly watched 50 to 100 times am glad some teachers helped in social media for other students to learn once again thank you sir ❤️🔥💝

@arslanakram8314 4 года назад

sir, you are doing great in explaining bioinformatics stuff. please make detail video on Drug designing and admet analysis. Thanks alot.

@infomen8128 3 года назад

I have similar technical tutorials please check it

@chemistryforall-bynsridhara 2 года назад

thank you sir for this valuable tutorial your videos are very clear and easy to understand these helped me alot

@y.mauriciomunoz-munoz9990 2 года назад

Thank you very much for your video! Greatings from Germany :)

@kassangoyekoumbamureillene5335 Год назад

thanks very much for this tutorial

@rashamoustafa427 11 месяцев назад

Many thanks 🎉🎉for the great work and explanation 👍 😊

@ofosuhemaajoyce9478 Месяц назад

If I may know why did you select a specific chain

@sibtulhassanshah2990 6 месяцев назад

Make a clear cut video of cuda installation with gromacs why you skip that portion?

@ummatilawan5797 Год назад

Very interesting Please my question is that can I install both LAMMP and Gromacs at same time in windows?

@jaykay383 Год назад

Amazing teaching skills. Salute your acumen. However, need some guidance. Stuck at 8:16 moment of this video. Kindly elaborate it a little, how can i find path in my desktop. Gromacs was downloaded by sudo apt-get install gromacs, but i dont know where it has disappeared in the desktop

@akundel 3 года назад

You are an amazing teacher! I have watched so many of your videos. You have the best explanations and most easy to follow directions. Thanks so much for all your help! One extra help, have you ever done Charmm-gui to gromacs? There is only one video and it is in Spanish:) Thanks for all you do:)

@jaannawaz2007 3 года назад

Glad you like them!... soon i will upload video MD simulation on different forcefield

@cukoosaartworld 3 года назад

@@jaannawaz2007l

@castilloh.gianmarco1048 3 года назад

Wow, amazing video gg.. 😍 👌 Thanks channel.

@jaannawaz2007 3 года назад

Thank you so much 🤗

@prakashj7199 2 месяца назад

If you are a long time Linux/*nix user, you may backport latest gromacs from Debian Sid repository and rebuild it from the sources.

@mobasserhosain5446 Год назад

Sir what is minimum hardware requirement for run MD 200ns per day?

@oktavialisti172 2 года назад

thank you for yiour video SIR, canwe form the topology using Charm-Gui force field for gromacs input?

@shamalasham102 Год назад

Sir, is it possible to do molecular simulations for protein-protein complexes? if yes, kindly share the online server and applications for protein-protein simulations

@prakashmurugesanprakash392 Год назад

sir, can you tell me your laptop model??

@johirislam8174 3 года назад

The PCA and free energy-based analysis to understand the correlation of atomic movements in the vaccine-receptor complexes and Free-energy based binding energy calculations (MM-PBSA/GBSA).How can i perform both of them??

@phdstudentsviews3667 5 месяцев назад

Can you please tell me how to run gromacs in could Google colab platform

@ayeshaafzal4884 2 года назад

Great work man. Is there any online tool for converting my .edr files to .xvg for graph visualization?

@sehrishkakakhel3643 4 месяца назад

Can we run in Intel gpu

@nehaverma4519 3 года назад

after launching ubuntu its not showing me id and pswrd thing...its showing me error..plz help me with it

@youssefennaji1585 3 года назад

thank you for the illustrations, is there any working online server for Gromacs or for energy minimization calculation?

@jaannawaz2007 3 года назад

NoMad-Ref

@rezafazl9024 Год назад

HI sir, If I runnig a complex simulation, Can I go to my other work with the system at the same time?

@arjunsankhla1035 2 года назад

How to resolve hash mismatch error while running sudo make command?

@toylemmons9320 11 месяцев назад

I tried you command line installation of GROMACS, but it installs it the 2020 version, and not the latest version. How might I install the latest version via the command line? Thank you so much in advance!

@sandipghosh5760 4 года назад

Hello sir.. can you please make a video on ligand based docking or docking based inverse virtual screening to identify the potential active sites for a ligand.

@infomen8128 3 года назад

I have similar technical tutorials please check it

@hanstsahnang4533 2 года назад

Thanks for the tutorial it actually helped me to Install gromacs but immediately I close my terminal , and open it back, as I hit gmx the message which appears on the terminal is "gmx command not found , use sudo apt get install to download the command gmx". Which is not normal as I go the build directory as I hit gmx is still get the same message as cited above what's the real problem since I installed gromacs successfully.

@kashafrasul3952 9 месяцев назад

perfect

@swarnadabral 7 месяцев назад

Sir, my laptop has 16 gb RAM and 1 Tb ssd. I've removed hard drive to put ssd. Can install linux and gromacs and run md simulation with these system requirements?

@the12nina 3 года назад

I'm trying to install gromacs with gpu acceleration using WSL2, but running into some errors, have you ever tried it? I really need some help with it

@pushkardiwakar9740 Год назад

sir i do not have GPU in my computer, Will this software work?

@dileepdn9464 3 года назад

Hi sir, I am trying to identify the CHRAMm forcefield of different bases using Discovery studio visualizer, but i am not able to obtain required data from it. can you please help me out of it sir.

@gopishankar1121 4 года назад

sir i hve 8gb ram and 2 gb graphics card with 512gb ssd so can i run gromacs in this sepcs

@jaannawaz2007 4 года назад

Hi, to be frank it's not a good idea to run MD in low configured systems and laptops, generally MD need to run ECC RAM machines (servers, HPCs) to get accurate results. As everyone doesn't have accession to HPC, we are compiled to use PC. The above PC configuration is not good enough to run MD, if u wish to run ur system will hang and it will take lot of time to run .

@muhammadrezkirasyak 3 года назад

Sir if i already installed cuda, gpu and gromacs, how to activating my gou for run my simulation?

@poojakumawat9960 Год назад

Can I get a help? I followed this vedio for gromacs installation. But, GMX program is using only one core (% memory 1) out of 18 core CPU, so the computation is very slow. Please suggest me how to use multi-core of cpu for gmx program calculation in Linux environment.

@mansi9799 Год назад

please suggest a server that can create topology files for my ligand. I am using Gromos force field. the prodrg server is unavailable.

@syifasilfani1858 2 года назад

My laptop didnt fulfill the system requirrements as yours. is it still can run if my specs are i5, hdd 500 gb, 8gb ram, and Windows 10. Type of my laptop is Lenovo T420 from the year of 2011 . Thank you

@duc-hainguyen8499 2 года назад

Dear Sir, could you help me with issue. After I run this command. gmx pdb2gmx -f modified -o 1.gro -p 1.top -water spce I have this issue: File input/output error: 1.top

@al-baghdadibaraaadilhadipm1222 3 года назад

hello everyone, hope all are doing fine... how can I run a MD 10 nm?

@gahinde8500 3 года назад

Sir can we use this in I5

@ASTUDIO-official Год назад

sir where is spdbv software link please mension it ...

@ravibalaskar3496 4 года назад

Hello Sir I have Intel core i5 processor, 8 gb Ram, 2 gb Intel and 2 gb nvidia graphic card, 1 TB HDD, can I run MD simulation using gromacs or any other software

@jaannawaz2007 4 года назад

@laibarajput3878 Год назад

can i install on i5?

@sethupathiraj 2 года назад

Sir what was the water model used in the procedure

@sethupathiraj 2 года назад

Is it tip3p, tip4p, spc/c

@MSL-MGA Год назад

hello sir , I am not able to set password in ubuntu.

@s.kulshrestha3298 3 года назад

From which link can I download spdbv? I can't find the link in description. Plz help.

@jaannawaz2007 3 года назад

spdbv.vital-it.ch/download_prerelease.html

@fadovni9341 Год назад

@@jaannawaz2007 hello sir, this link is not available thank you

@shuvrohafij759 3 года назад

Is graphics card compulsory for MDS, i have core i5 integrated graphics.

@jaannawaz2007 3 года назад

not advisable to run MD simulation on Laptops ... for longer and reliable results u have to work workstation or servers... if u dont have options at least u need i7 10th Gen 32GB RAM, 8GB graphic Card, 1 TBSSD system

@user-mo3lr2xy8e 3 года назад

After the installation and typing “dir” all i can see is error, how can fix this? Another thing please sir, if i wanted to launch gromacs through their way “as in the website” do i have to download some cmake files? Because when i run it the process appears to be incomplete

@enseignante6444 3 года назад

Are you used Windows pro?

@sarthakmohanty997 2 года назад

I have a Windows 10 system with the NVIDIA RTX 3060 GPU (6 GB). Will it be possible for me to run GROMACS using my GPU? If yes, then can someone please guide me on how to do it?

@shaileshmanitripathi9888 3 года назад

I am getting error while executing the pdb2gmx command the fatal error is Atom P in residue G 1 Was not found in rtp entry RG5 with 32 atoms while sorting atoms.. Please help how to rectify this error

@infomen8128 3 года назад

I have similar technical tutorials please check it

@jameelabduljalil25 3 года назад

Hello professor I hope you are doing well Can my laptop (specifications below) cope up with GROMACS as a part of protein-ligand drug discovery work? Windows 7 Intel(R) Core i7-4500 CPU 1.8 GHz RAM: 6 GB System type 64-bit Graphic card: 1696 MB Intel(R) HD Graphics Family

@jaannawaz2007 3 года назад

Actually.. its not adavicable to run MD simulation on Laptops ... for longer and relaible results u have to work workstation or servers... if u dont have options at least u need i7 10th Gen 32GB RAM, 8GB graphic Card, 1 TBSSD system

@jameelabduljalil25 3 года назад

@@jaannawaz2007 Could you please recommend a reliable server for MD simulation? Thank you in advanced, sir.

@jaannawaz2007 3 года назад

@@jameelabduljalil25 Check this article ...www.mdpi.com/2079-9292/10/2/185

@jananikarthikeyan6604 3 года назад

When I downlaod the source code, it was downlaoded in pdf format rather than a tar format, could you kindly give a solution for this.

@jaannawaz2007 3 года назад

u maight have selected pdf program as default to open tar file. try this Right click on the file select the default program winrar or winzip

@auliafauzy 3 года назад

Hi sir, I'm going to run this on core i7, 16 GB RAM, 1TB HD, 2 GB Intel 4600 GPU and 8 GB Radeon R9 380 GPU PC is the running still going to take so much time?

@jaannawaz2007 3 года назад

if u have accession to cloud service or high end server prefer to go for it. if u dont have option, u can run MD with above configuration, but not advisable for long run it will hang ur PC and u cant open any other programs...

@amina5075 2 года назад

Can any one please explain what is 2DAD at 8:11 minutes. I am not getting it

@fadovni9341 Год назад

it is the name of your username

@misslojyn2829 3 года назад

ir i hve intel (R) core (tm) i5-8250 U 8gb ram and intel(R) UHD graphics 620 total memory 4gb Ram(physical memory )=8go Total virtual memory = 13.8go Availaible memory = 10.1 go So can i run gromacs in this sepcs ? and i used gaussian and if i can not what i do ? Thabk you

@jaannawaz2007 3 года назад

@misslojyn2829 3 года назад

@@jaannawaz2007 even if I have 27 or 39 atom and if I add 8GB on my pc it does not exist ?

@jianhuazeng8156 3 года назад

could you help me，I can’t open desktop

@infomen8128 3 года назад

I have similar technical tutorials please check it

@muhammadhaseeb3032 Год назад

Hi! Sir, I am continuously facing an error each time I run a command and provide a directory to the folder I am working with. It gives an error of "too many arguments." Is there any solution to this? cd / cd mnt/c/Users/MUHAMMAD HASEEB/Desktop/MDS/ It gives the error that I mentioned above.