@@Bioinformaticswithbb 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
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 ❤️🔥💝
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
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:)
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
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
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!
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??
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?
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 .
When i use "pdb2gmx -f x.pdb ... NOw, i m getting a warm : "Fatal error: Residue 'UNK' not found in residue topology database." then when I delete the UNK part in pdb file.. there is no warm and error from this code. how to solve this problem while the "pdb2gmx -f ....." is used without not delete the ligands from the pdb file?..thanks
To solve the UNK residue issue in GROMACS, parameterize the ligand using tools like acpype, PRODRG, or CHARMM-GUI to generate a topology file (.itp). Rename UNK in the PDB file to the ligand name used in the topology (e.g., LIG). Include the ligand topology (#include "ligand.itp") in your system .top file and list it in the [ molecules ] section. Run pdb2gmx again with the updated files to avoid errors. .. hope it will fix
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.
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.
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
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.
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
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
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 .
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.
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
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
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?
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
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
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
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
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?
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...
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.
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!
You're very welcome!
@@Bioinformaticswithbb 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
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 ❤️🔥💝
Thank you very much for your video! Greatings from Germany :)
sir, you are doing great in explaining bioinformatics stuff. please make detail video on Drug designing and admet analysis. Thanks alot.
I have similar technical tutorials please check it
Many thanks 🎉🎉for the great work and explanation 👍 😊
thank you sir for this valuable tutorial
your videos are very clear and easy to understand
these helped me alot
thanks very much for this tutorial
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
Wow, amazing video gg..
😍 👌 Thanks channel.
Thank you so much 🤗
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:)
Glad you like them!... soon i will upload video MD simulation on different forcefield
@@Bioinformaticswithbbl
Very interesting
Please my question is that can I install both LAMMP and Gromacs at same time in windows?
Sir what is minimum hardware requirement for run MD 200ns per day?
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
If I may know why did you select a specific chain
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
HI sir, If I runnig a complex simulation, Can I go to my other work with the system at the same time?
Make a clear cut video of cuda installation with gromacs why you skip that portion?
after launching ubuntu its not showing me id and pswrd thing...its showing me error..plz help me with it
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!
If you are a long time Linux/*nix user, you may backport latest gromacs from Debian Sid repository and rebuild it from the sources.
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??
thank you for the illustrations, is there any working online server for Gromacs or for energy minimization calculation?
NoMad-Ref
thank you for yiour video SIR, canwe form the topology using Charm-Gui force field for gromacs input?
Can we run in Intel gpu
Sir My Ubuntu is showing failed to download one component what should I do ?? please sir Assist me
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?
sir i hve 8gb ram and 2 gb graphics card with 512gb ssd so can i run gromacs in this sepcs
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 .
When i use "pdb2gmx -f x.pdb ... NOw, i m getting a warm : "Fatal error: Residue 'UNK' not found in residue topology database." then when I delete the UNK part in pdb file.. there is no warm and error from this code. how to solve this problem while the "pdb2gmx -f ....." is used without not delete the ligands from the pdb file?..thanks
To solve the UNK residue issue in GROMACS, parameterize the ligand using tools like acpype, PRODRG, or CHARMM-GUI to generate a topology file (.itp). Rename UNK in the PDB file to the ligand name used in the topology (e.g., LIG). Include the ligand topology (#include "ligand.itp") in your system .top file and list it in the [ molecules ] section. Run pdb2gmx again with the updated files to avoid errors. .. hope it will fix
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.
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.
How to resolve hash mismatch error while running sudo make command?
Can any one please explain what is 2DAD at 8:11 minutes. I am not getting it
it is the name of your username
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
sir where is spdbv software link
please mension it ...
Great work man. Is there any online tool for converting my .edr files to .xvg for graph visualization?
please suggest a server that can create topology files for my ligand. I am using Gromos force field. the prodrg server is unavailable.
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
sir, can you tell me your laptop model??
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.
I have similar technical tutorials please check it
sir i do not have GPU in my computer, Will this software work?
Can you please tell me how to run gromacs in could Google colab platform
From which link can I download spdbv? I can't find the link in description. Plz help.
spdbv.vital-it.ch/download_prerelease.html
@@Bioinformaticswithbb hello sir, this link is not available thank you
Sir if i already installed cuda, gpu and gromacs, how to activating my gou for run my simulation?
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
Are you used Windows pro?
can i install on i5?
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
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 .
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.
perfect
Sir can we use this in I5
hello everyone, hope all are doing fine... how can I run a MD 10 nm?
hello sir , I am not able to set password in ubuntu.
Sir what was the water model used in the procedure
Is it tip3p, tip4p, spc/c
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
I have similar technical tutorials please check it
Is graphics card compulsory for MDS, i have core i5 integrated graphics.
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
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.
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
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?
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
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
@@Bioinformaticswithbb even if I have 27 or 39 atom and if I add 8GB on my pc it does not exist ?
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
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
@@Bioinformaticswithbb
Could you please recommend a reliable server for MD simulation?
Thank you in advanced, sir.
@@jameelabduljalil25 Check this article ...www.mdpi.com/2079-9292/10/2/185
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?
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...
could you help me，I can’t open desktop
I have similar technical tutorials please check it
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.