Hi, very nice quick intro. It would be more helpful for the users if you demonstrate HREX with REST2 with any software of your choice, if possible gromacs.
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!
clear and conceptual explanations. thanks you
I'm happy you found it helpful!
extremely helpful and clear. thank you
I'm glad you found it helpful!
Thanks this was very helpful
Glad to help!
Hi, very nice quick intro.
It would be more helpful for the users if you demonstrate HREX with REST2 with any software of your choice, if possible gromacs.
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