Molecular Dynamics

Development
1

Hi,

The conjugated gradients algorithm has been replaced by a molecular
dynamics option. This is probably not the right place for this
(altough this might be usefull in his current and simple form to
simulate simple things like a water molecule). It probably deserves
it’s own tool where you can record and play back trajectories. I
haven’t looked at the code yet, but does OB support trajectories?

Is anyone working on this, I saw it is on the todo list. Or does
someone need special features? Comment on the description below if you
had visioned the implementation differently.

Here is a desciption of how I think the tool could be implemented:
a slider (min=1, max=number of frames)
a row with buttons: [ << ] [ < ] [ [] ] [ | | |> ] [ > ] [ >> ]
below setting to do MD simulations:

  • temperature
  • timestep (=0.001ps)
  • steps
  • button “simulate” (this would open a file dialog (trajectory
    filename), start the MD simulation and show progressbar)

Tim

2

Hi Tim,

simulate simple things like a water molecule). It probably deserves
it’s own tool where you can record and play back trajectories. I
haven’t looked at the code yet, but does OB support trajectories?

I think this is definitely a separate tool to record and play back
trajectories. Open Babel supports trajectories in the same way as
conformers. In both cases, you have the same molecular system, but
with multiple coordinate “frames.”

One caveat. Currently Open Babel does not support any trajectory
formats like CHARMM. That’s mostly a minor issue – writing one would
be pretty easy.

  • button “simulate” (this would open a file dialog (trajectory
    filename), start the MD simulation and show progressbar)

I think we might also want a way to open an existing trajectory/
animation file and play it back with the same tool.

I don’t know of anyone working on this right now. It was put onto the
TODO list as a cool idea that we should do sometime in the future. :slight_smile:

Cheers,
-Geoff