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It's always nice to see new people getting interested in computational chemistry! If you like you can write me on Facebook, but as I do it in my free time I do not connect to it very often facebook.com/thecomputationalchemist/ BTW have you already given a look to my other videos about MD? th-cam.com/play/PLMRj3zlKNpjHHBYdUWZ_mjsWgT8xHnpcF.html And here you can find some very well done tutorials on how to run simulations in many commonly used MD programs www.mdtutorials.com/ While for a more in depth view on the theory you might want to check out these two books Computer simulations of liquids, and Understanding molecular dynamics

Hi, I am not sure I got your comment, are you planning to print yourself a T-shirt about PME, or are you telling me that the process of printing a shirt is similar to PME?

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@@PhDFood Cool, I didn't know!

Hi, those seem like CMake flags, it looks like you are describing the level of optimization of the code you are looking for -O3 and then there are some info about the CPU and the computer architecture. In any case this stuff varies a lot from program to program, so the best thing is to always read the documentation where the relevant CMake options should be described in detail.

Thank you!!

I'm happy you found it helpful!

I'm glad you found it useful!

Hi! If in the first step you were using an enhanced sampling algorithm that does not respect the Boltzmann distribution (eg MetaDynamics, Opes) you would indeed have to reweight the contribution to the final free energy of every configuration you use as a starting point to the alchemical transformations. But in this case, as we are using a method that respects the Boltzmann distribution, by randomly extracting the starting configurations from the Hamiltonian replica exchange, the free energy result can be used without the need for a reweighting (more probable conformations will naturally be more present in the extracted frames than less probable ones).

Hi! At the moment none of these are on my radar, but in case I'll let you know! For the synthesis part I'd suggest you to look for someone who is better tailored for it, my area of expertise is computational chemistry not synthetic chemistry.

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Glad to help!

Thank you for the positive feedback!

Thank you!

I am not sure I understood the question right, does this paper contain the answer you are looking for? doi.org/10.1145/3096742

I'm glad you found it helpful!

Thank you very much for the nice feedback!

Thank you a lot!

Thank you for the feedback!

Thank you!

You're welcome!

I am glad you find it helpful!

Hi! I am not sure that I understood your question, but maybe the generic video I did about alchemical transformations might help th-cam.com/video/ypg1doAqVPM/w-d-xo.html Let me know if it answered your question

Hi! I personally never worked with PMF so I won't be able to fully help you on this. But in any case, as it looks like your doubts are more technical than theoretical, with a quick google search I found this links that might be useful manual.gromacs.org/current/reference-manual/special/free-energy-pmf.html www.mdtutorials.com/gmx/umbrella/index.html (the second one is part of a website that contains a lot of very useful gromacs tutorials). In general for technical questions on how to do something with a specific MD program the program documentation, research gate ( www.researchgate.net/ ), facebook groups (like this one for example facebook.com/groups/373718163121955 ), and YT tutorials (if available) can go a long way. If on the other side you are looking for a theoretical overview on PMF there is something on at least one of the books I have put in the description of the video. About the Hamiltonian, in short it's the energy of the system, if you like to know more I did a video about it th-cam.com/video/ZNs64W4DMhk/w-d-xo.html and the video is part of a playlist I did on analytical mechanics th-cam.com/video/IygyBuESixY/w-d-xo.html If you would like a more physics oriented explanation I usually find Andrew Dotson's videos very intuitive to understand th-cam.com/users/AndrewDotsonvideos And I also noticed that TMP Chem has some videos about the quantum chemical Hamiltonian of a molecule if you are interested (but remember that in MD we use classical mechanics and not quantum, so this would be simply a plus for curiosity) th-cam.com/users/TMPChem

@@thecomputationalchemist Thank you soo much sir..

Thank you a lot for the nice feedback, and I'm very happy it helped you!

I'm glad you found it helpful!

Thank you a lot!

I am happy I have been able to help!

Hi! This is a one million dollar question, different methods have different pro and cons, give you different information and might be better suited for different systems. And as many of the binding free energy methods are still continuously improved and developed things might change. So I am afraid that there is no shortcut to knowing, trying and studying the different methods and keeping updated on the literature. In any case as I have been using non equilibrium alchemical transformations a lot any answer I would give you would be very biased in that direction.

Thank you very much for your nice feedback!

Hi, that's a very good idea for a future video! In any case if you need to run a replica exchange with solute tempering with gromacs you need to patch your gromacs with plumed and then follow what's written in the documentation www.plumed.org/ the process is a bit complex to do but the documentation is well written. This is the paper where Bussi describes how he implemented it in plumed (what is scaled and what isn't) www.tandfonline.com/doi/full/10.1080/00268976.2013.824126 To make things more automatic I actually recently did a small python package github.com/MauriceKarrenbrock/HREMGromacs and if you need to scale a ligand in a protein pocket and its first neighboring residues with this small program you will get everything set up automatically github.com/MauriceKarrenbrock/HPC_Drug I hope this helped and have a nice day!

@@thecomputationalchemist Hi Maurice, thanks, i went through HREMGromacs module in your github page. Which version of gromacs with which plumed version works best with your package? Could you kindly add a tutorial document (stepwise explanation on how to run the calculation) using your package. Alternatively, a youtube tutorial video, just like this one, will also be helpful. Thanks a lot.

@@sinhasuman1944 It should work with any gromacs version that is supported by the latest plumed version. I have personally been using gromacs2019 but it is for totally unrelated reasons. Adding some instructions on the README is on my to do list, but I am pretty busy at the moment, so it might take a while. In any case if you read the plumed documentation on parallel tempering it will become pretty obvious to understand what the functions do and which ones you personally need. In any case if in the future you end up creating a nice example script that you would like to share I will be more than happy to receive your pull request on github. Have a nice day!

@@thecomputationalchemist thank you so much. Sure, why not, I have just started reading about it, i might be a long journey for me too

Thank you very much for the feedback!

Hi, thank you very much! If you like you can write me on Facebook facebook.com/thecomputationalchemist/ BTW have you already given a look to my previous videos about MD? Maybe the answer that you are looking for is already there ;) th-cam.com/play/PLMRj3zlKNpjHHBYdUWZ_mjsWgT8xHnpcF.html

@@thecomputationalchemist Thank you sir🙏

Thank you very much!