Thank you for such a nice presentation. I was trying MD which was seemingly difficult for me. After seeing this presentation I got a lot of understanding. thank you so much
Hi Aleksandar, thanks a lot for your tutorial but a I have a big doubt. How have you created the file topol.top? You don't write any output comand with -o topol.top and suddendly you use it when solvate molecules. I am having a lot of problems with topology, a little help will be welcome. Thanks :D
I got the same problem while performing the simulation. After that, I saw couple of sample .top files and wrote one my own. I believe, the topol.top file has to be written by the person who performs the experiment.
You can see the contents of topol.top file that has been used by him at 31:34. Just create a file with the name topol.top and write the displayed content on the file.
Greetings from Brazil! I would like to see something about comparative modelling (i´m a begginer in computational biology). Thanks a lot for this presetantion!
good video, however I am doing it to the letter and an error appears when adding the ions, it says that there is an error in the recognition of the atoms ... for help. Thank you
Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products
why I can’t produce mdp format in gromax? in all my reserch, see downlod links of ions. mdp for lyzozim. but i want produce that is or find mdp format for every protein. please, help me. thank you so much.
hiiiii thnx for the tutorial. I am beginner to GROMACS. I was unable to understand how u got the all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top. Please help!!!!!!!
Hi, all of these files are simple text files, which I have created some time ago, and just reuse/modify whenever I need them. You can find the files used in the presentation in the Virtual Sim Lab webpage.
@@aleksandarmehandzhiyski2964.... can u teach me how can i generate or create all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top for my molecule.
