submission of amber MD simulation jobs to gpus on nmrbox

[srinivas penumutchu]

Hello NMRBOX team,

I am running sander.MPI (AMBER), if i would like to submit the jobs to gpu on nmrbox, what are the commands that i should use ?.

if i am right,  sander.MPI alone should work or  should I use nice command  (nice sander.MPI) ?. 

I also came to know that there is no pmemd or pmemd.cuda (amber)  modules are not avilable on nmr box, these modules can speed up the simualtions.

Thank you !

 

[Mark Maciejewski]

Srinivas,

 

Unfortunately at this time we do not have the GPU version for AMBER. Ambertools is free for academic and non-profit use and includes sander and that is what we have installed in NMRbox. However, the GPU enhanced version of AMBER is not free and we have not yet purchased a copy to include in NMRbox at this time.

 

Sorry the news is not better with regard to speeding up sander. Maybe we can examine this in the future, but that would be a ways off.

 

Mark

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