Hello, it seems all the trajectory snapshot structure downloaded are the same, either by get a trajectory snapshot or by get a trajectory fragment operation. Can I get structure of a particular snapshot, like #500? Thanks!
Hi,
yes, the operations you mentioned (in particular the trajectory snapshot structure), allow the extraction of one single snapshot. If the snapshot given as a result is always the same, it could be that the input trajectory only has one snapshot. Try to download the trajectory and explore that. Was the trajectory generated with an MDWeb setup workflow? In this case, it can have just one snapshot, as these workflows were designed to prepare a system to be used as an input for a MD simulation, but not to run a production MD. More information in this thread: Limited Molecular Dynamics Simulation Time.
I would also recommend you to take a look at the BioExcel Building Blocks (biobb) website and its associated BioBB-Wfs server (Homepage - BioExcel Building Blocks Workflows)), which are more recent tools that can help you on the MD setup and run processes.
Thanks for your interest in our tools!
Regards,
-Adam-
Hello Adam,
Thank you for your reply. Yes, the trajectory was generated with an about 8-hours NPT simulation (500ps) using the Gromacs Full MD setup workflow. Is this work a 500ps MD production or still configuration files? what the one snapshot represents, the last (#500) or the input (#0) structure? What the average structure represents? It seems the snapshot, the average, and the input structure are all different.
Thanks,
Leila 
Hi Leila,
the Gromacs Full MD setup workflow is just preparing the system to be used as an input for a production MD simulation. It is not generating the 500ps MD production. For that, you can either download all the generated files and run the simulation in your own premises, or run a short simulation (up to 500ps) in the MDWeb infrastructure. You can follow the MDWeb Run Tutorial.
Now, the last (#500), the input (#0) and the average structures extracted from the resulting setup trajectory are giving you the last, first, and average structure of a really short (1ps) simulation which is the last step of the setup process. It is not a production MD and is not giving you any information about the flexibility of your system. They are just representing equilibrated conformations of your starting structure. To obtain a more representative set of conformations and explore the conformational landscape of your system, you should run a longer MD simulation.
Here again, I strongly recommend you to take a look at the BioExcel Building Blocks (BioBB) website and in particular at its associated BioBB-Wfs server (Homepage - BioExcel Building Blocks Workflows), which will give you more clues and tools to properly run a MD simulation in your own premises.
Thanks again for your interest in our tools and I hope this information will help you!
Regards,
-Adam-
Hi Adam:
Thank you for the information!
Leila