@@hardlearner Thank you, sorry one more question, how can I decide how long do I need to run my simulation? Is 1 million steps simulation will be enough? I used VMD-NAMD
@@a21-izzati39 hi Izzati no worries. so the length of simulation depends on what you're trying to see. For example I run peptide membrane interaction for those I run 1-2 microseconds. Because I wanna see how the peptide inserts and all which takes time. For some of my retinal molecule in gas phase I only run 3ns. Because I only interested to see the methyl group rotations and bond length alternation. 1 million means if the time step is 1, you're running a 1ns simulation. So if you see whatever the events you're expecting then you're good. Longer the better. But again there is a trade off by your computer timing and resources. Check literature on your type simulations, to see how long others have run. Does that make sense?
@@hardlearner I see, understood.Thanks! Sorry I am still newbie with vmd and namd. I would like to ask for your opinion. Currently, I study the effect of mutation of the protein towards the binding affinity of a ligand. Prior molecular dynamic, I did molecular docking simulation and I found out that the binding affinity of the ligand towards the mutated protein does not differ much in term of binding affinity from the wild type.They only differ by 0.1. If I were to do molecular dynamic, what is the outcomes that I can expect for? Is it the RMSD and RMSF? I have seen few study related to study of effect of mutation towards protein, they find rmsd and rmsf value and this result they relate to the binding affinity of the ligand towards the protein. Their result of molecular docking shows different binding affinity when compared between mutated and the wild structure. My question is, in my case, since after molecular docking, the mutated protein binding affinity towards the ligand doesnt change much, what outcomes can I expect for? What are the among outcomes that I can analyse to see the effect of the mutation? Sorry for the long questions, and thanks a lot!
@@a21-izzati39 im familiar with RMSD but not RMSF. RMSD gives the difference between two structures whether your structure after mutation is stable or not these kind of infor. After docking if you know these infor, then MD can be used to validate the docking studies by showing the similar result. Or MD shows you the real time whats happening. So either you can see how the H-bonds are affected from this mutation, how the solvent accessible surface area (SASA) changes.. since I'm not working with mutations or ligands my answer may not be complete. Have you seen a fb group for docking and molecular dynamics? You can get more comments in the group if you post there too.
Can we select any solvent/mixture of solvents for solvating? I am seeing only water in most of the cases. If possible how to do it?
Concentration 1.5 is a bit steep! Someone might even use this number. People normally use 0.15.
Pls you have any idea for calculating hbonding between protein-lind for each frame
Umm I haven’t done it but let me check that
Sorry I have questions, then you will use the ionised psf and pdb file right as input for the md simulation? Not the solvated one right?
Yes correct
@@hardlearner Thank you, sorry one more question, how can I decide how long do I need to run my simulation? Is 1 million steps simulation will be enough? I used VMD-NAMD
@@a21-izzati39 hi Izzati no worries. so the length of simulation depends on what you're trying to see. For example I run peptide membrane interaction for those I run 1-2 microseconds. Because I wanna see how the peptide inserts and all which takes time.
For some of my retinal molecule in gas phase I only run 3ns. Because I only interested to see the methyl group rotations and bond length alternation.
1 million means if the time step is 1, you're running a 1ns simulation. So if you see whatever the events you're expecting then you're good. Longer the better. But again there is a trade off by your computer timing and resources.
Check literature on your type simulations, to see how long others have run. Does that make sense?
@@hardlearner I see, understood.Thanks! Sorry I am still newbie with vmd and namd. I would like to ask for your opinion. Currently, I study the effect of mutation of the protein towards the binding affinity of a ligand. Prior molecular dynamic, I did molecular docking simulation and I found out that the binding affinity of the ligand towards the mutated protein does not differ much in term of binding affinity from the wild type.They only differ by 0.1. If I were to do molecular dynamic, what is the outcomes that I can expect for? Is it the RMSD and RMSF? I have seen few study related to study of effect of mutation towards protein, they find rmsd and rmsf value and this result they relate to the binding affinity of the ligand towards the protein. Their result of molecular docking shows different binding affinity when compared between mutated and the wild structure. My question is, in my case, since after molecular docking, the mutated protein binding affinity towards the ligand doesnt change much, what outcomes can I expect for? What are the among outcomes that I can analyse to see the effect of the mutation?
Sorry for the long questions, and thanks a lot!
@@a21-izzati39 im familiar with RMSD but not RMSF. RMSD gives the difference between two structures whether your structure after mutation is stable or not these kind of infor. After docking if you know these infor, then MD can be used to validate the docking studies by showing the similar result. Or MD shows you the real time whats happening. So either you can see how the H-bonds are affected from this mutation, how the solvent accessible surface area (SASA) changes.. since I'm not working with mutations or ligands my answer may not be complete. Have you seen a fb group for docking and molecular dynamics? You can get more comments in the group if you post there too.