[AMBER] MD under external electric field & GPUs parallel problem

From: <wumeng.shanghaitech.edu.cn>
Date: Tue, 2 May 2017 09:28:29 +0000

Dear All,

 I am studying a channel protein and I want to apply the external electric field(E) in the channel direction(z) to drive the substrate molecules pass through. I have noticed "efz, efn, efphase, effreq" mdin parameters(only accessible in Amber16 and not in Amber14? ) in the Amber16 manual, but I am not sure if these are exactly what I want, if yes, how to set them in general.

 By the way, I have another problem about GPUs parallel met before. There are 4 GPUs/node in our lab, when I use two of them ("export CUDA_VISIBLE_DEVICES=0,1/2,3 mpirun -np 2 pmemd.cuda.MPI -O ..." ), the speed is normal; but when I use all("export CUDA_VISIBLE_DEVICES=0,1,2,3 mpirun -np 4 pmemd.cuda.MPI -O ..."") , the speed dropped dramatically. I don't know what's the problem in and how to deal with it if I want to use 4 GPUs in parallel to get a higher speed.

  Any suggestions would be greatly appreciated.Thank you in advance!

All the best,
Wu Meng
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Received on Tue May 02 2017 - 02:30:02 PDT
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