Hello! The process of using PLUMED with pmemd programs is the same as
for sander: specify "plumed = 1, plumedfile = 'plumed.dat'" in your mdin
config, do "export PLUMED_KERNEL=/path/to/the/libplumedKernel.so" and
run your MD simulation as usual. I assume that you've already compiled
AMBER with PLUMED support: for Amber18 you should use patch from PLUMED
distro while since Amber20 PLUMED support is integrated into AMBER
distrib already. Also please remember that for MPI versions of
sander/pmemd you should export proper PLUMED kernel built with MPI
support too.
-------- Original message --------
> Hi everyone,
>
> Thanks a lot for your continued support and help! It's giving me more things to test and move ahead with my work :)
>
> I have another question. Our group is looking into running Steered MD using PLUMED in Amber. We've been looking into how to use it, and we know it works in Sander. However, we want to use it with GPU acceleration, but can't seem to find any tutorials on how to integrate PLUMED with pmemd.cuda. Does anyone know of any we could work through/could point us in the right direction?
>
> Best wishes
>
> Amanda
>
>
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--
73, Viktor
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Received on Fri Jun 05 2020 - 03:00:02 PDT
