Dear AMBER developer
I have to do MD simulation of protein-metal ion complex employing bonded
model MD simulation. I have generated topology file for the bonded model.
When I am using CPU for calculations, its working fine but when using GPU
its showing problem
"3086: 6179 - 6180 and 3088: 6178 - 6180
Hydrogen atom 6180 appears to have multiple bonds to atoms 6179 and 6180
which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
I have checked the protein-metal ion complex after 10 ns production run of
CPU calculations and its looking fine.
So, please suggest how to solve this SHAKEH problem.
In case if I will opt CPU for final calculation. Will it affect my expected
result?
With regards
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Received on Tue Nov 21 2017 - 02:30:02 PST
