Search found 63 matches
- Thu Apr 22, 2021 7:04 pm
- Forum: OpenMM
- Topic: velocities not written to DCD
- Replies: 9
- Views: 328
Re: velocities not written to DCD
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 ...
- Wed Apr 21, 2021 6:01 pm
- Forum: OpenMM
- Topic: velocities not written to DCD
- Replies: 9
- Views: 328
Re: velocities not written to DCD
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...
- Mon Dec 07, 2020 6:13 pm
- Forum: OpenMM
- Topic: OpenMM 7.5 release candidate
- Replies: 1
- Views: 193
Re: OpenMM 7.5 release candidate
Thanks, this makes life a lot easier!
- Wed Oct 21, 2020 7:31 pm
- Forum: OpenMM
- Topic: Guidelines on setting ewaldErrorTolerance
- Replies: 1
- Views: 78
Guidelines on setting ewaldErrorTolerance
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...
- Tue Oct 20, 2020 8:29 pm
- Forum: OpenMM
- Topic: OpenMM MM/GBSA calculations
- Replies: 6
- Views: 392
Re: OpenMM MM/GBSA calculations
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
https://github.com/ljmartin/mmpbsa_from_openmm
- Tue Oct 20, 2020 3:45 pm
- Forum: OpenMM
- Topic: OpenMM MM/GBSA calculations
- Replies: 6
- Views: 392
Re: OpenMM MM/GBSA calculations
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. -...
- Mon Oct 19, 2020 5:12 pm
- Forum: OpenMM
- Topic: metadynamics
- Replies: 1
- Views: 197
Re: metadynamics
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...
- Wed Jul 29, 2020 4:27 pm
- Forum: OpenMM
- Topic: Minimum distance to a group of atoms as a collective variable
- Replies: 3
- Views: 155
Re: Minimum distance to a group of atoms as a collective variable
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...
- Tue Jul 28, 2020 5:25 pm
- Forum: OpenMM
- Topic: Minimum distance to a group of atoms as a collective variable
- Replies: 3
- Views: 155
Re: Minimum distance to a group of atoms as a collective variable
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...
- Mon Jul 27, 2020 9:55 pm
- Forum: OpenMM
- Topic: Minimum distance to a group of atoms as a collective variable
- Replies: 3
- Views: 155
Minimum distance to a group of atoms as a collective variable
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...