search

Autodesk / molecular-simulation-tools

Web applications for molecular modeling using the Molecular Design Toolkit
http://molsim.bionano.autodesk.com
Apache License 2.0
16 stars 10 forks source link

SHAKE in LAMMPS #241

Open avirshup opened 7 years ago

avirshup commented 7 years ago

Dave to devote some time to figuring out SHAKE in LAMMPS so that we can increase the timestep from 1 -> 2 fs

Once figured out, work with Day on Autodesk/molecular-simulation-tools#212

dane1122 commented 7 years ago

@avirshup Shake does work - I can shake hydrogens with the command fix shake-hydrogen all shake 0.0001 20 10 m 1.0 ; but sometimes the simulation becomes unstable (which we can't really do anything about) and it crashes.

If you are okay with that, I can push it to master

ktbolt commented 7 years ago

The simulations Da was doing used an NVT thermostat which created very unstable simulations; I could only run a few hundred time steps with a 1 fs time step before the simulation crashed.

Using a Langevin thermostat (with NVE) and shake produced stable simulations with a 2 fs time step.