Introduction to practical MD Simulation in GROMACS

I am thankful to Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry (www.mdtutorials...) for providing the tutorial on their website. You can visit this website for a complete intro.
"*.mdp"Files used in this video can be downloaded from following links. Right click and click "save link as" in the simulations folder.
ions.mdp = raw.githubuser...
minim.mdp = raw.githubuser...
nvt.mdp = raw.githubuser...
npt.mdp = raw.githubuser...
md.mdp = raw.githubuser...

[@sibsankarkundu1728]

Great video !!! The most important point is that everything is working !!! Much better than many others. I have checked all the comments and your replies to the queries. Thanks a lot !!!

[@OfficialSaypeople]

Very illustrative presentation.... could help the beginners....

[@DrRehanZafar]

Thank you Usman

[@suyashpant6007]

One of the best tutorial for beginners. Sir, can you provide similar kind of presentation for supervised molecular dynamics

[@user-dx4ei8qt2h]

hi sir How does one extend the protein simulation in Gromacs ? for exemple 50ns finished and i want to extend it to another 50ns ? thanks in advance.

[@lifefunny6352]

Good information thanks

[@shilpinagpal1738]

I am a complete novice using windows. I understand the basics theoretically, but am scared to do things on my own in computer. How to begin.

[@saintgloirebimbadi2269]

this is the topic of my master degree. i know that lysozyme in water is for beginners but i want to have a solid work with the same protein

[@al-baghdadibaraaadilhadipm1222]

so nice tutorial, I have a question here.. is there any possibilty to run a PTM for specific residues in pdb file via GROMACS?

[@DrRehanZafar]

Gromacs could use PTMs for their effects on the dynamics of a system. However, it would be great to use DFT analysis for transformation of one molecule to another.

[@pallaviagrawal208]

ions.mdp file is not form.. when I give commant gedit 1AKI_solv.gro

[@DrRehanZafar]

No ions.mdp should be in the folder. I can provide it if you want. Gedit is only to look into the file structure of gro.

[@shivu2213]

How can I change the temperature from 300K to for example 400K? I need to see what the effects of temperature are on the protein. Which files should I edit?

[@DrRehanZafar]

In MD simulation, see .mdp file of MD and search for "ref_t = 300". Change it to 400. Why you are doing this and what other factors are involved, I am leaving it to you.

[@armichaudhary8445]

Hello sir I am doing protein rna simulation in gromcas while using gmx command to generate gro file it is giving error like protein residue A does not find in rwsidue topology database

[@DrRehanZafar]

Definitely the nucleotides of RNA or some modified residue in the protein can cause this kind of problem. See the tutorials for adding modified residues in the topology of the protein. For now, I am very busy in the projects, you can search in Research gate. As soon as I could take my time out then I will make the tutorial on this problem as well. I hope you can understand.

[@zenabmalik7207]

Great lecture sir..very helpful

[@DrRehanZafar]

Thank you Zenab

[@monalishapattnaik3941]

which force field must be used for multi lipid layers or multi lipid liposomes?? how can we use the martini force field as they are no option coming?

[@DrRehanZafar]

You can use gromos 53a6 but the itp files for each lipid type must be addressed in toplogy.top file. Martini can also be used. Simply, put the martini force fields related files in some folder and use custom force fields in flags of gromacs commands. I have not tried martini so far but hope that same process may be used.

[@sapnamahera4172]

While running tpr file we are getting faltal error too many warnings? Can u resolve it

[@DrRehanZafar]

Most probably, the topology or input file is not formed correctly. Due to which this error is coming. Following command should be used to see what is happening in TPR. gmx dump -s topol.tpr | more gmx dump reads a run input file (.tpa/.tpr/.tpb), a trajectory (.trj/.trr/.xtc), an energy file (.ene/.edr), or a checkpoint file (.cpt) and prints that to standard output in a readable format

[@zamirhussain3451]

Very informative

[@johirislam8174]

Can you kindly send me the PCA analysis code and MMPBSA code of linux ,so that i can run my MD trajectory files .I used CHARAM force field for that.

[@DrRehanZafar]

For PCA analysis, see MDANALYSIS (userguide.mdanalysis.org/dev/examples/analysis/reduced_dimensions/pca.html). However, MMPBSA analysis could be performed by using GMMPBSA (rashmikumari.github.io/g_mmpbsa/). Plz check whether this one is also working for the latest version of gromacs.

[@johirislam8174]

@@DrRehanZafar is there any vedio behind that??Becuase i donot actually perform Linux or python properly.

[@saintgloirebimbadi2269]

hello sir, i studed lysozyme in water with gromacs and i did not found more results.i want to have more results about that protein.what parameters can i change?

[@DrRehanZafar]

What type of results do you want to analyse on this protein?

[@aqsakhalid2194]

Gromacs consider protein in vaccum so it do not consider the periodic boundary conditions of its replicates... This is the drawback right?

[@DrRehanZafar]

Please send me the reference where it is written that Gromacs consider the protein in vacuum as this is not the case according to my understandings. Moreover, plz clarify so that I could help you.

[@aqsakhalid2194]

@@DrRehanZafar thank you for your response.... Actually when I prepare the files for MD. The script for Minimization consider only PBC of protein not the replicates of that protein. This creates confusion in my mind whether it consider PBC of its replicates or not. As in the script file the replicates of that protein is not considered. It is what I understand. I would appreciate if u help me to clear this confusion.

[@DrRehanZafar]

Without seeing the system, it will be difficult to suggest anything. If you are around then show me the system.

[@aqsakhalid2194]

@@DrRehanZafar thank u so much

[@johirislam8174]

my laptop configuration is 4GP,HARDISK 1TERA,I5 GENERATION.Can i able to perform MD simulations with that configuration??Besides i want to increase my ram upto 8gp and try to add SSD

[@DrRehanZafar]

Yes

[@johirislam8174]

@@DrRehanZafar Sir i increase my ram upto 16gp and add 480gp ssd but my laptop is DDR3. So can i perform gromacs with that.

[@DrRehanZafar]

Good.

[@johirislam8174]

@@DrRehanZafar thanks sir but can gromacs run in that configuration?

[@Dark-tk9xu]

I want to study the binding energy between a protein and different 'gold' surfaces..I have the .psf file of the protein.. Could you make a relevant tutorial? Thanking you in anticipation..

[@DrRehanZafar]

Gold surfaces against protein are simulated better in dlpoly and other programs. I will try but not sure at this time that when will the video be made.

[@sufyanrazzaq8650]

It's really helpful and really Thanks Sir ❤️

[@DrRehanZafar]

More are on their ways.

[@DrRehanZafar]

Thank you

[@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?

[@DrRehanZafar]

It depends on several things that what do you want to achieve. However, the difference between the algorithm for simulations may be different but there is no difference at technical levels according to my experience.

[@fahimalamnobel4789]

@@DrRehanZafar Thank you very much, sir, for your reply. I want to know another thing. Sir, I want to upgrade my laptop configuration. I am running i5, ram 4gp harddisk 1tera. My laptop is generation 5. How much configuration may boost my laptop with high speed so that I can run Linux, MD simulation, virtual screening and others bioinformatics work so easily without hanging my laptop by the grace of Almighty Allah.Thanks in Advance

[@rameshjethara588]

Is it good for md simulation of protein on i5 for thesis student or not ? If not which processor can we use?

[@DrRehanZafar]

You can run small simulation on i5. However, only problem is that you should not leave such simulations running on the laptops unattended for a long time. Moreover, it is better if you have GPUs on desktops so that the simulation can be completed in lesser time. Please see the usage of GPUs in gromacs.

[@rameshjethara588]

@@DrRehanZafar thank you

[@user-uz3ox4tx3y]

atom N not found in buiding block 1ACE while combining tdb and rtp HOW TO SOLVE sir

[@DrRehanZafar]

Mostly, this happens when some terminal amino acid is not fully buit, like in your case. So see -ter flag at this link manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html

[@fahimalamnobel4789]

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

[@DrRehanZafar]

Yes it is good for start but you need Ubuntu alongside windows either in virtual box or just install it alongside. Do it carefully if you do not know that how to install ubuntu alongside of windows.

[@fahimalamnobel4789]

@@DrRehanZafar sir i want to install ubuntu into my windows.But i want to know that when i start MD simulation into my pc,will this configuration support me to do MD simulation completely?? In my pc there is no extra gpu or any other graphics card.There is a simple configuration that is i5,ram=4gp,hardisk =1tera. I want to do MD simulation of ligand and receptor. If this so then how much time will take to do that and is any hampered will occur into my windows or other software when i perform that.

[@kalsoomjan8516]

Can we use it for MD simulations of metal organic framework?

[@DrRehanZafar]

I have not found gromacs good at metal organic frameworks. However, try it yourself. Moreover for metal organic frameworks are rather good in AMBER, CHARMM, DLPOLY ETC.

[@kalsoomjan8516]

@@DrRehanZafar Thank you sir.

[@Flower_here]

Good doctor Reha

[@Flower_here]

Rehan

[@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

[@DrRehanZafar]

You are right you have to use gromos43a1p forcefield (ffG43a1p.tar.gz or gromos43a1p-4.5.1.tgz) which already contains the information about phosphorylated Ser, Tyr, Thr. www.gromacs.org/Downloads/User_contributions/Force_fields For this, follow the following steps and let me know: 1- Unarchive the force field tarball in your working directory: tar -zxvf gromos43a1p-4.5.1.tgz There should now be a "gromos43a1p.ff" subdirectory in your working directory. In later steps, the structure will be processed by pdb2gmx, and you will be prompted to choose a force field: >>> Select the Force Field: From current directory: 1: This is that one --> gromos43a1p.ff From '/usr/local/gromacs/share/gromacs/top': 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) Select "1" and that is all. :)

[@nadataib348]

@@DrRehanZafar Thank you very much, I 'm very pleased with your clear and didactic explanations.

[@nadataib348]

@@DrRehanZafar Dear sir, Thank you for your response, I still have a problem when I run gmx pdb2gmx for my protein which contains TPO and MS and I don't know how to solve this problem which is blocking me. Thank you very much for your help: Start terminus LEU-331: NH3+ End terminus LEU-637: COO- ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1.4 Source code file: /home/nada/Téléchargements/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746 Fatal error: Atom OCT1 in residue GLN 669 was not found in rtp entry GLN with 12 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at www.gromacs.org/Documentation/Errors

[@DrRehanZafar]

@@nadataib348 The extra oxygen atom of the carboxy terminal amino acid is designated as OXT according to PDB rules whereas in your PDB, the last residue GLN 669 is having a type of nonstandard convention i.e. OCT1. You can change the atom name to OXT and then try the same commands for GROMACS. Plz remember to make a copy of the PDB before doing this. If you want to confirm it then here is the link with page number: cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1996.pdf Page Number: 189 (Terminal oxygen atoms are presented as OXT for proteins, and as O5T or O3T for nucleic acids //// it is recommended that the C-terminus atoms be labelled O and OXT) Page Number: 190 (For proteins, there is usually a terminal oxygen, labeled OXT) Page Number 206. Just finding OXT with CTRL+F in the document. :) Moreover, when you open the pdb in Notepad++ then you may find it like: ATOM ? OCT1 GLN ? 669 ? ? ? ? ? ?. Question marks represents variables.

[@nadataib348]

​ @@DrRehanZafar Dear Sir, Thank you very much for your answers. I'm sorry to bother you again. I did as you told me for my protein which contains a TPO residue at position 638, but it seems that gromacs ignores this residue and considers that the COO- is at residue 637 knowing that in my repertoire I have gromos43a1p.ff . Je suis vraiment dans une impasse.

[@suchitraajjarapu9194]

sir, how much time will it take for a single protein analysis on i5 processor?

[@DrRehanZafar]

It depends upon the size of protein and time of Md Simulation step. Overall for 1ns Md it will take some hours.

[@suchitraajjarapu9194]

@@DrRehanZafar i have 14 protein structures with same 480 amino acid length, to be simulated with 1 week of time, does this gets finished? whats your opinion of online servers for dynamic studies? How much do they differ from gromacs? can u suggest me any?

[@DrRehanZafar]

Try your best by simulating one protein after the other. It should be finished before a a week, if you are considering md simulations of 1ns (Recommended 10ns or more).

[@ankitapanghal03]

From where to download the nvt.gro file?

[@DrRehanZafar]

Isn't it in the description? If not I will put that in the description of the videos as well. Thanks for asking.

[@mni79]

great

[@DrRehanZafar]

Thank you

[@abdullahiftikhar3982]

Background music is fantastic 👌

[@DrRehanZafar]

Would you like more?

[@abdullahiftikhar3982]

Yeah sure

[@debanjansen1282]

and sir if upload a tutorial for g_mmgbsa it will be helpful... as in in whole KZbin there is limited tutorial on gromacs based mmgbsa tutorial

[@DrRehanZafar]

Sure soon

[@SuperSupergenious]

@@DrRehanZafar still waiting Sir.

[@DrRehanZafar]

@@SuperSupergenious I am planning.

[@debanjansen1282]

sir, Mere pass ek inclussion complex hain... uske liea MD karna chatahun.... sir guest and host ke liyea to swissparam se parameter generate kar sakte hain.... magar... host ke liyea pdb 2gmx script kam nei kar rahan hain.... to sir host.gro, topol.top, purser.itp yea sab file kaise generate karun...want to use charmm36

[@DrRehanZafar]

For inclusion complexes, you should either use CHARMM software or AMBER. Moreover, DL_POLY software should be used to effectively simulate the inclusion complex. With all of the these you can easily generate the forcefields of the guest and host molecules. I will soon make a video on these type of complexes as well.

[@debanjansen1282]

sir, can u share your mdp files??

[@DrRehanZafar]

Sure

[@DrRehanZafar]

Will add the links to the description of the video.

[@DrRehanZafar]

Links to the mdp files have been added to the description.

[@aqsakhalid2194]

Please guide me in this

[@lifefunny6352]

Good information thanks

[@DrRehanZafar]

So nice of you