My bad, looks like AMBER can write velocities to a netcdf file ( https://ambermd.org/FileFormats.php#trajectory ) but perhaps the MDTraj NetCDF writer doesn't do a similar thing since I see no mention of 'velocities' in the code: https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/netcdf.py ...

DCD files don't specify velocities - the `velocities: bool` in the MDTraj docs was probably intended for the other reporters like HDF5Reporter or NetCDFReporter, either of which can store velocities. So if you wanted to store the velocities alongside the trajectory, use one of those. But if you're s...

Thanks, this makes life a lot easier!

Hi all, Is there a set of guidelines for changing ewaldErrorTolerance and changing the nonbonded cutoff to increase simulation speed? I'm considering a simulation where I just push everything to its limit or beyond to points considered not very sensible. One of the easy knobs to twist is to "just in...

Actually I wanted to do this for a while so here's a repo demonstrating how to use OpenForceField, OpenMM, and CaFE to run an MMPBSA estimate of the binding affinity of catechol to T4 Lysozyme

https://github.com/ljmartin/mmpbsa_from_openmm

I think that's referring to estimating free energies of ligand binding using MMPBSA. Since this is a post-processing technique, Osvaldo you can use any of the analysis toolkits out there on the trajectories you generate with OpenMM: -For example MMPBSA.py from the AMBER toolkit like you mentioned. -...

The custom force in this case never gets added to the system directly, it's just used by the metadynamics module to calculate the value of the collective variable. So you want the energy expression to evaluate to the the value of the collective variable. To do this, change force = CustomBondForce("k...

OK I tested it out by adding forces that calculate minimum distance of a sodium ion to both the upper and lower leaflets of a CHARMMGUI lipid bilayer. If anyone's interested, see a notebook here: https://github.com/ljmartin/lipid_diffusion_colvar_example/blob/master/lipid_diffusion_colvar_example.ip...

Thanks Peter. I think to get a reasonably sized membrane I would need around 64 lipids per leaflet, so one restraint per headgroup, and then two leaflets, is 128 bonds. Surely that would be less extra distance calculation than adding even a single extra lipid. Anyways Ill drop a gist here later with...

Hi all, Is it possible to define a custom force as the minimum distance between one atom and a group of atoms, or alternatively a molecule COM and a group of atoms? The purpose is to use minimum distance to lipid headgroups as a collective variable for ligand diffusion across the bilayer, for exampl...