Molecular Dynamics Tutorial | Lysozyme in Water: GROMACS - PART 1

[@sachinbhogyan2521]

It is one of the easiest and simplest way to learn MD. thanks

[@AmanUllah-tk6wt]

I have two more questions if you could kindly entertain them. 1) Is server necessary to perform MDS? or one can perform on PC? 2) What should be the specs of a PC which could perform MDS? Thanks in advance sir

[@baischoice1743]

Great job Sir. Thank you for sharing your knowledge.

[@blackraven7492]

Thank you for turorial! It was very useful

[@darkfernando02]

Thank you! Very useful and innovative way to learn

[@faisalfadzil9883]

Thank you! U answered some of my questions

[@sakshisharma9192]

It was really easy and useful 😊

[@shivshankargupta4107]

Really very good and understandable video.

[@AmanUllah-tk6wt]

I have two more questions if you could kindly entertain them. 1) Is server necessary to perform MDS? or one can perform on PC? 2) What should be the specs of a PC which could perform MDS? Thanks in advance sir

[@lalaladygirl5805]

Hi Sanket, is it possible to make a video on using the gmx make_ndex tool? I want to analyze separate parts of the protein but I can't figure out how to! Thank u!

[@DrHenryNguyen]

@Sanket Bapat 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

[@JohnGabriel-e2o]

Hello sir. Can Molecular Dynamics simulation be used to provide insights about the outcomes of CRISPR-Cas9 correction of a certain variant?

[@meghnaroy7774]

Thank you so much

[@NurArshad]

hi, is there any tutorials to perform MD for protein-protein complex?

[@SwatiKumari-pl6zg]

thank you for the great explanation, please make a video of virtual screening by using ZINC database

[@anushkagarhwal9629]

Sir can you please explain how can we run gromacs using supercomputer. Please make a detailed video on this.

[@radhapanchanathan4870]

Thank you so much for this video. it's really really helpful. In the same way, Could you make the analyzing results (RMSD, RMSF, hbond, binding energy)videos if possible!!

[@johirislam8174]

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).I want to perform both.But how can i do that.And which of your lecture will help to perform that??

[@vindujaram8239]

Thank you sir. It is highly informative. Kindly let me know is there any video on the installation of GROMACS in Linux from your side?

[@sanketbapat]

Will do that

[@andresjvazquez]

@@sanketbapat You have no idea how much you saved me with this video (I truly am grateful! 🙏🙇‍♂️)

[@guadalupeflorian7913]

Thank you so much!

[@hamzadar9021]

Please guide me on how to simulate Protein-Protein docked complex using Gromacs. I read online that I need to follow Lysozyme tutorial but this method is only for simulating one protein structure.

[@sanjaisrao484]

Sir what should we do for md sim of protein-protein docking complex?

[@包伊丽]

Thank you for this great tutorial!! What if I want a visualized video result of my protein, is that possible to get that ?

[@lotfibourougaa6209]

I made MD for two complex with same protein (with gromacs). I got RMSD of backbone protein (complex 1) deferent to RMSD of backbone protein (complex2).. despite the two MDs were for the same condition. Which backbone protein RMSD should I take?

[@shubhraverma9664]

Can you please after performing all step in terminal how you open the structure ?

[@PRIYANKACHOUDHARY-du2pf]

thank you sir! I have a query, why you have used different force-fields for same protein in both the tutorials 1)lysozyme in water and 2) protein-ligand complex.

[@swatideshmukh7708]

Hello sir, I have started learning gromacs and your videos really helped me alot. In my analysis, when i applied certain elwctric field to protein, the solute was not inside the solvent but shifted aside. Am I going in wrong direction???

[@nadataib348]

Thank you for this great tutorial. Sir i want to simulate a protein with phosphorylated residues, i use gromacs 5 but i don't know how to do it? i don't know how to implement gromos43a1p to gromos57a7. thank you

[@vindujaram8239]

Sir, while downloading a protein structure from pdb,. It may contain water molecules,inbuilt ligand and some other ions. So whether we have to remove all these things before doing MD for apo-protein?

[@veekshithakesana4010]

Sir what is periodic boundary concept? Why it's necessary for simulation?

[@shourjoprakash9802]

Sir, do I have to memorize all those big big codes that you are typing?!

[@ikhsansantuy4686]

do you have the video that explain Biphasic system

[@vindujaram8239]

Hi sir, I have the latest version of GROMACS (2020). Can I use the GROMACS tutorial that you have mentioned? Because it's for 2018 version.

[@walia5555]

Sir i have one problem. I am using a pdb file for docking in which one amino acids is replace with formylglycine and further convert into disulfate form. I am new in this field but i am doing docking but only problem occur in these step can you tell how to add and which free software used for it

[@mamoonariffat5080]

How you visualize it at the end??

[@jarosawserafin7865]

Hi Sanket great tutorial. I have more questions can we talk on priv?

[@swatideshmukh7708]

Thank u very much!!!

[@sanjaysharma9751]

Mam kya aap bata sakti han ki kis software par sir apna code likh rahe han

[@swatideshmukh7708]

@@sanjaysharma9751 He is using basic commands of Gromacs software in Linux operating system.

[@alishafazil7756]

Sir aapne vo box ur solvation dekhn ke liy kism open kiy hai please usk name bataye clearly nhi dikh rha video me

[@vikramgaikwad2599]

Thanks

[@raqshiqishraaq8740]

dear sir, I would be really grateful if you made a video about how to modify the forcefields. Lot of people are now trying to model biomolecular interaction with metal surfaces. However, they are unable to do so because they don't know how to change the force field parameters in gromacs. If you showed us this it would be a great help.

[@sanketbapat]

Modify force fields means, I am not getting it.

[@SandeepYadav-ni5eu]

Sir one of my protein is not creating xxxx_processed.gro and no data in topological file. What should I do? Please help me.

[@rahulrathore1368]

are we not able to perform gromacs MD in windows operating system.

[@veekshithakesana4010]

Sir how to install VMD? Which linux version are you using? And which gromacs version?

[@fahimalamnobel4789]

Sir i want to perform MD simulation but i want to know how much minimum configuration is needed to do MD simulation.My pc configuraion is i5,ram 4gp,hardisk 1 tera and i am running windows 10pro.?

[@enseignante6444]

Hi i hve lenovo laptop 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 to calculate 39 or 27 atom? Thank you

[@andrianduda4751]

Sir, I have issue for the gmx command. Gmx: command not found

[@andrianduda4751]

How to solve this issue?

[@RakeshBhowmick]

Sir, i have DNA bound to protein pdb file. Can I directly run simulation in Gromacs? Which force field can I use for this complex?

[@sanketbapat]

Yes

[@sheetaldhiman8762]

Glucagon is recognized by cells using a G-protein-coupled receptor. This receptor is a bit different than a typical GPCR, like the one that recognizes adrenaline. It has an extra domain on the outer side of the cell , which traps glucagon and delivers it to the membrane-spanning portion. When glucagon binds, it activates G-proteins inside the cell, starting off a cascade of responses that lead to release of glucose. Find out the secondary structural changes in terms of RMSF of the protein complex in the membrane. Sir can you help me that how to solve this question

[@sanketbapat]

Check the links, you will understand how to generate RMSD. www.researchgate.net/post/How_to_determine_protein_stability_using_GROMACS www.mdtutorials.com/gmx/lysozyme/index.html

[@sheetaldhiman8762]

@@sanketbapat 😞😞😞no idea sr

[@faisalshahzad7837]

kia ye window 10 p. operate ho skta ha

[@joshhayden1706]

Hi there, love the video! Was wondering, have you ever encountered a problem where the command line will not reappear after completing each step of the tutorial? I've had to abort gromacs and restart everytime to use the command line again for some reason.

[@sanketbapat]

Thank you, No I have not encountered anything as such.

[@enseignante6444]

Hi 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 ? Thank you

[@fahimalamnobel4789]

Hello, sir, I want to do molecular dynamics of an epitope and its receptor. sir what kind of pc configuration I need to do that.My pc configuration is i5,ram-4gp,harddisk-1tera.Is programming is needed to do that?

[@sanketbapat]

Yes, the simulation may take time but.

[@fahimalamnobel4789]

@@sanketbapat Sorry I am not clear out of your answer? Can you plz tell me in details. May I do this into my PC(the configuration I give above) and if I cannot do this into my pc so what kind of pc configuration I need to do MD simulations.

[@explore_with_pinku]

Thank you sir for this videos 😊 Sir I have a question is it possible to run GROMACS MD simulation in Windows operating system ?

[@sanketbapat]

No works on Linux

[@shvel1648]

www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_system_Can_anyone_help_me_with_a_step_by_step_tutorial

[@H_Vli_]

You can make a virtual Linux on your windows operating system. This is what I did. It will work with Linux syntax and you can instal GROMACS and do the same steps for simulation.

[@rajatranjan974]

Sir, can GROMACS software work on windows OS? Sir, Which programming language is required to perform molecular dynamics simulation?

[@sanketbapat]

Gromacs is the software... No different language as such

[@saboor_saifi]

Sir I am new to md simulations so can u pls tell me that how to download gromacs on window10??

[@nehaverma4519]

Why their is error in opening pdb downloaded file

[@sanjaysharma9751]

Sir kya aap bata sakti han ki kis software par sir apna code likh rahe han

[@sanketbapat]

Software ka naam GROMACS hai

[@fahimalamnobel4789]

I want to know something about MD simulation. Sir, I did MD simulation by desmond by the grace of Almighty Allah. Sir I would like to know what is the difference between GROMACS & DESMOND. Is gromacs gives a better result than desmond?

[@srijamukherjee1394]

can you please tell the system requirement?

[@sanketbapat]

I have made a video on the system requirement, you can check the videos

[@walia5555]

Sir What's is your email id

[@ekingursoz]

thank you so much.