Discussion around computational chemistry and cheminformatics tools for the Galaxy platform
doesn't help with the workflow extraction issue though :/
I am not sure about your underlying issue
I would not use it
but i get this error when i run it
"The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below."
were u able to run it after dragging and dropping?
interesting that
prmtop doesn't appear in the upload menu as a datatype option
I wonder if that's related
how did you manage to set the datatype then?
you can rerun that history and see what it does
if u rerun step 16
I wonder if the extensions are really not enabled somehow on EU, if nothing is working
it seems it was merged into the right repo, _release_21.09_europe
ok, our sysadmin Gianmauro is looking at it, apparently they are indeed missing
@thepineapplepirate in future, we need to edit https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/config/datatypes_conf.xml for the changes to be shown on EU
I haven't touched that file for a couple of years, I forgot that it existed 😅
so in the case of new datatypes
as well as this
is that why prmtop and inpcrd weren't showing up?
the one in the Galaxy repo is the default configuration, but we are overriding it on EU with our own config file
hence why both need to be updated
@bhagirathbhatta838 On second thought, Langevin dynamics ('integrator = sd' in your mdp file) should be ok in this scenario. But in general it's worth keeping tabs on the integrators you use. Langevin dynamics is stochastic, which adds a degree of randomness into the system, and thus creates a simulation that is not entirely deterministic. This is done to help ensure constant temperature. In a real finite system, the atomic and molecular collisions would eventually lead to heat losses/gains that would influence a fluctuation in temperature. Langevin dynamics creates a 'dampening effect' at every time step, that helps reduce this loss, thus helping maintain constant temperature. you can think of this as greasing bearings in a wheel, a lubrication so to speak. regular md is ok, but for big systems that you are trying to simulate for longer periods of time, Langevin dynamics might be a good option.
that might be interesting for us :)
quite a nice library
not sure if it makes sense to be wrapped in Galaxy though