I also trust you shall make an elaborated video on MM PBSA/GBSA methods by using gromacs files because many a time peer reviewers are insisting to perform these calculations. Thanks
it was a very helpful session. please keep making such content. please make more videos on gromacs (other chemical systems, their analysis, and free energy and trajectory-based calculations).
Thank you for such a insightful session professor , it will be really helpful if you can show us how to perform MMPBSA BFE calculations using Gromacs for the complexes Thank you in advance
Hi, I want to run simulation on GPU but I am unable to configure GPU during Gromax installation. Basically Gromax is not detecting my GPU. On other side, I am using Desmond on same system and there is no any issue in performing simulation. Please guide me about how to configure GPU on Gromax.
Nice explaination. I have obtained dipole moment of a molecule using gromacs, but how I can visualize it in vmd as a vector along with my molecule. Should i give this dipole.xvg file as an input to vmd???
Hi dear Please I need to ask you about dipole moment What is important to calculate it in MD simulation process What is the idea that I get form dipole moment value ?? Thank you dear
The command that ordered to calculate rmsd between ligand and protein by vmd in tutorial is protein or resname K23 is that true Please anyone correct me
If the gromacs has been compiled with GPU during installation, but default, mdrun launches the run on both CPU and GPU so no extra steps are necessary. Nevertheless, to specify number cores or GPU or the tasks that need to be offloaded to GPU can be set by various parameters like -nt for number of cpu threads , -gpu_id to specify a gpu, -nb gpu to offload non-bonded calculations to GPU.. etc
my protein have zinc ion and hydroxide ion. i tried all type of forcefield but i could not run simulation it shows error zn residues not found or oh residue not found. did you have any suggestion for run my protein.
Is there any scientific report describing the Gromacs parameter used for this Protein-Ligand Molecular Dynamic Simulation? In the affirmative, could you indicate the title from the paper or where to find more pieces of information about it since on the Gromacs Tutorials website there are no indications of literature. Thank you :)
Hi.. thanks for this comment. Yes it works definitely help to such guide and honestly, i don't have any such material. My understanding of parameters has come from trial and error with the list of parameters and their descriptions given at gromacs reference site manual.gromacs.org/documentation/2018/user-guide/mdp-options.html but I'll surely search for something useful and if not, it would be a good ideas write such
sir, I have a problem and i need your help. I did MD simulation of protein ligand complex and now doing post MD analysis ie calculating RMSD, RMSF, SASA Rg etc but sir i don't have an idea of selecting different groups for protein ligand complex analysis.if you can share material with me regarding this problem then it would be helpful.
Actually both are exactly same group of atoms.. the way groups are listed here is K23 is listed once under *Other* type amd once under *Non-water* because it comes under both.. any one of those cam be selected..
There is something I just realized. npt.xtc and nvt.xtc files are not created as a result of the calculation made with the gmx grompp -f npt.mdp..... and gmx grompp -f nvt.mdp...... commands. What could be the reason for this? . As a result of the calculation made with only the grompp -f md.mdp command, md_lig.xtc is formed.
XTC are compressed trajectory files.. usually production runs are much larger in size, i use parameter to save XTC files only in production run. In NVT and NPT files, only TRR files are produced as their mdp files don't contain flag for XTC (nstxout-compressed)
Sir is it safe to run GROMACS in laptop.. I have a HP Omen gaming laptop. Can I use it for simulation? or running simulations will affect its hardware?
It is safe to do so but always make sure while simulation is running, your laptop is around a good ventilation or under a fan or AC as it gets heated up running for several days.. typically for small simulations, it's not at all a problem to run on laptop.. it won't affect the hardware
I commend "gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0" for solvation, But there is showing error is this , "Source file: src/gromacs/fileio/groio.cpp (line 67) Fatal error: gro file does not have the number of atoms on the second line." How can i solve it. I have wrote the sum at the second line of complex.gro file
hello dear sir, im trying to add ions on my protein ligand system and i get following error: Fatal error: Syntax error - File LIG_GMX.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes i used the acpype server to build the ligand topology. how can i solve this problem. thanks
For actype, the inclusion of itp file should be at different position in topology file. It should be at the top region, after protein force field is included before the [atomtypes] directive starts
gmx trjconv -s md_lig.tpr -f md_lig.xtc -o md_corrected.xtc -pbc mol -ur compact in this command i am unable to chose two group together can you tell me how to chose protein and ligand both I tried with 1|13 i also tried with 1&13
You need to also provide index (ndx) file containing the group definition of protein and ligand with -n flag. If you already have not prepared the index group, you can do so by gmx make_ndx command
PDBQT file is format used specifically by AutoDock and Vina so you'll first need to convert it into standard PDB format, which can be done using Chimera, AutoDockTools etc. This PDB file then can be used to generate .gro and .itp files. I assume it's a ligand, so you can follow the same procedure used in video to generate .gro and .itp files depending on force field you're using (PRODRG for gromos, CGenFF for charmm, LigParGen for OPLS).. all of these online tools will give you necessary input for gromacs
Sir I am stuck at energy minimisation step, it's only doing till step 12 and error is as follows: Recieve buffer size too small for transmission (in valid comm) Aborted (core dumped) Please help. Thanks in advance.
Hello this cold be because if the forces generated.. did you get any other message before this part? Like bad contacts or unsettled atoms? You can share your structure and mdp file to be more helpful
@@jiteshvdoshi sir, for another pdb I tried md run... it's coming: step xyz will no longer try dynamic load balancing, as it degraded performance....is my md still running? And what does this mean?
Hello.. the files used have been linked in the description.. from rcsb, you can also get the file with id 3LBK and then separate the protein (mdm) amd ligand (k23) into 2 files..
@@jiteshvdoshi I am using same config..but i am getting speed near 30 ns per day.. but in your tutorial it was showing around 120.. My gpu is enable Cuda.. can u tell me reason behind it..why my speed it slow? does speed rate depend on the molecule?
@@Hammad187 Are you working with same protein as in tutorial? Because performance highly depends on size of the system. Also, how did you install gromacs? Gromacs need to be compiled with -DGMX_GPU=CUDA flag during installation. If you are using gromacson windows, it doesn't support GPU. To confirm, if your mdrun command is utilizing GPU or not, open the logfile of your mdrun and check the top portion..
hello dear prof thanks a lot for this tutorial. if i use amber to build the topology file of the ligand which file extension should i use to paste in the topol.top file. i generated the topology parm of ligand separately with amber18 i have the following extensions lig.lib lig.rst7 lig.parm7
gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr going through this comand gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'ns_type' NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1258424182 Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' ERROR 1 [file topol.top, line 10677]: No such moleculetype ligand There was 1 note ------------------------------------------------------- Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2511) Fatal error: There was 1 error in input file(s) Kindly help to rectify the above issue.
