Hi Mark,
To my knowledge, she's not using CHARMM-related FF's at all -- I think she
is using Amber03 (Alyssa, correct me if I'm wrong). Visually and RSMD-wise
the trajectory looks totally normal, but is there something specific I
should be looking for in the trajectory, either visually or quantita
Hi,
What does the trajectory look like before it crashes?
We did recently fix a bug relevant to simulations using CHARMM switching
functions on GPUs, if that could be an explanation. We will probably put
out a new 2018 version with that fix next week (or so).
Mark
On Thu., 14 Feb. 2019, 20:26 M
Hi all,
My student is trying to do a fairly straightforward MD simulation -- a
protein complex in water with ions with *no* pull coordinate. It's on an
NVidia GPU-based machine and we're running gromacs 2018.3.
About 65 ns into the simulation, it dies with:
"an atom moved too far between two do
