Thanks for making MDWeb available. Such an excellent service to the research community!
I am now trying to learn it so that I can use it to generate a RMSd plot for my docked compound.(Please forgive me if my question is silly - I should declare that I have zero knowledge/experience in MD. )
I could follow the steps in your tutorial up to the point where I downloaded a f01.moby.tgz file.
I would like to use MDWeb, not Gromacs, for analysis. So I guess the next step is to start a new project and choose Analysis (MD Trajectory). Base trajectory setting is where I started to get confused/lost.
Unzipped f01.moby.tgz does not contain an XTC file. Your tutorial has some info about XTC trajectory in the section “3. Uploading a trajectory”. Is that how I can create an XTC file? It seems to say that I should install Gromacs first. So I have installed Gromacs on my win10 laptop and I tried typing in trjconv… but it said “command not found”.
Also, there are multiple itp files in my unzipped f01.moby.tgz. Which should I upload? Or how should I determine which to upload?
I am stuck at this point. Could you help?
Thanks and have a good day!