After installing Amber20 in a GPU server using A100 card,
I tried a simulation of a bound structure of a certain protein-ligand.
Right after the simulation run started, the system began to be unstable.
When checking the output file, the energy profile of a simulation diverged
(**** were printed in vdw energy component) and some parts of a protein
were blown up (bounced off somewhere).
However, when I tried the same simulation with the same md preparation
files in the GPU server using V100 card, the simulation continued to
progress stably.
Because I followed the general protocol to prepare MD simulations for a
protein-ligand system and the protocol was tested in the other machines,
the preparation did not seem to have problems.
Also I checked the initial starting structure to remove the steric bump.
Are there any special issues that I should consider when installing Amber20
on A100 linux server?
Thanks
Jongyoung Joung
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Received on Sun Jun 13 2021 - 07:00:02 PDT
