On Wed, Feb 22, 2017, Alicia Merlino wrote:
> Dear David, the calculation crashes while reading atomic coordinates and
> velocities with the error message that I reported before.
>
> Executable path: pmemd.cuda
OK...now I see that you are running pmemd.cuda. Can you try a short
simulation using pmemd itself? Doesn't need to be very many steps: just
set ntpr=1 so you can see if the simulation gets started OK.
> >> >
> >> > 80: 177 - 178 and 81: 177 - 179
> >> > Hydrogen atom 177 appears to have multiple bonds to atoms 178 and 179
> >> which
> >> > is illegal for SHAKEH.
> >> > Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
> >>
Amber developers: does anyone know if the atom numbers printed here (from
gpu.cpp) start from zero or from 1?
....dac
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Received on Wed Feb 22 2017 - 18:30:03 PST
