Sir, thanks a lot for uploading an informative tutorial. Could you help me with this problem: I was following your steps until 7:28, I clicked OK and then MOE said "The time step is possibly too large or there is too much strain energy in the system". I chose the minimum time step (0.0005) but the notification still occured. How can I decrease the existing strain energy please? Btw, MD still runs if I don't add water molecules in the system. Could this possibly be a problem of my laptop, sir?
@@Coach.ismail I had selected energy minimization before docking ligand with protein. Here I'm presuming that you do MD right after docking (at the first of the video), or am I wrongly understanding your work, sir?
@@quangcuong3190 you have to do it again as previously you minimized the enrgy of protein only, and now you have ligand docked with it, and ligand form a pharmacore around the protein so some time it produce strain
Assalam-0-Alaikum Respected Sir Can you please tell which computer or laptop should i buy to run md of publication quality in good journal please share the details thanking in anticipation
Wasalam its depend on you budget, now a days GPU systems are being used but they are too much expensive, under CPU shoulf have at least 8th Generation or 10th generation system, with 8 or 10 CPUs, they will complete the 10ns job in 3,4 days approximately, it you increaze the Number of CPUs in a system the time will reduce, like a 32 CPUs system can run the same job in one day.
Informative and detailed
Thank you
Sir, thanks a lot for uploading an informative tutorial. Could you help me with this problem: I was following your steps until 7:28, I clicked OK and then MOE said "The time step is possibly too large or there is too much strain energy in the system". I chose the minimum time step (0.0005) but the notification still occured. How can I decrease the existing strain energy please?
Btw, MD still runs if I don't add water molecules in the system. Could this possibly be a problem of my laptop, sir?
1st you can go to compute option and select energy minimization. I hope this will resolve your issue.
@@Coach.ismail I had selected energy minimization before docking ligand with protein. Here I'm presuming that you do MD right after docking (at the first of the video), or am I wrongly understanding your work, sir?
@@quangcuong3190 you have to do it again as previously you minimized the enrgy of protein only, and now you have ligand docked with it, and ligand form a pharmacore around the protein so some time it produce strain
Assalam-0-Alaikum Respected Sir Can you please tell which computer or laptop should i buy to run md of publication quality in good journal please share the details thanking in anticipation
Wasalam its depend on you budget, now a days GPU systems are being used but they are too much expensive, under CPU shoulf have at least 8th Generation or 10th generation system, with 8 or 10 CPUs, they will complete the 10ns job in 3,4 days approximately, it you increaze the Number of CPUs in a system the time will reduce, like a 32 CPUs system can run the same job in one day.
@@Coach.ismail thankyou Sir...