Is there any way so that we can set the simulation time for a production run manually? For example, is it possible for me to run a simulation (production) for atleast 20000 ps? If yes, then how?
MDWeb was designed to be mainly a server to prepare MD simulations and run short equilibration runs, up to 500 ps, due to the limitations in computer resources. What you could do is to prepare the needed configuration files to run the simulation in your own premises. You can find all the information in the MDWeb Run tutorial.
I would also recommend to take a look at the BioExcel Building Blocks (biobb) website, which is a more recent library that can help you on the MD setup and run processes.
Thanks for your interest in our tools!
That means we can’t run production dynamics in the MDWeb server, am I correct?
And after performing a complete simulation run using the MDWeb, may I know which trajectory files are used for the RMSD and other analyses in the MDWeb server?
MDWeb generates different trajectory file formats, depending on the MD package used in the simulation. Accordingly, it also accepts different trajectory file formats for the analysis operations. You can find all the information in the operations help section, including the programs used for the analyses and the accepted formats.
For example, for the RMSd analysis:
Root Mean Square deviation along the trajectory.
Programs: Ptraj from AmberTools package (Binpos,Crd,DCD,NetCDF trajectory formats). g_rms from Gromacs package (XTC trajectory format).
Hope it helps!
Correct, what MDWeb offers is (apart from the previous complete setup of the structure) an easy way to generate the needed configuration files to run the simulation in different MD packages that you can then download and use in your own computers. All the information can be found in the help pages.
The x-axis of the RMSD along the trajectory plot shows snapshots. I thought the x-axis would have shown time. Does the snapshots represent the time?
Yes, snapshots represent the time. As MDWeb doesn’t know how much time the snapshots of the input trajectory represent (in most of the cases), it just puts the snapshots in the x-axis.