[gmx-users] Results of villin headpiece with AMD 8 core

[Wahab Mirco]

Hi Paul,

thanks for your reply.

On 11.01.2019 23:20, paul buscemi wrote:
> Getting the ion and SOL concentration correct in the top is trickier ( for me ) than it should have been,   If you happen to  reuse  both  solvate and genion during  the build  keeping track of the top is like using a digital rubics cube..!  The charge  the villin was +1 because after I downloaded it from the pdb I removed all other water and ions - it just made pdb2gmx easier to work with.
> 

I simply hand-edited the .gro by making up two ions and put them
somewhere near the corners and added a short energy minimization.
Then, I added one line in the .top for the ions.

> The 1080 scaled nicely with the 1080 ti,  these are really nice pieces of hardware. and you are correct, given the choice of increased processors vs  faster processors - choose the latter. I have the AMD OC to 4.0 GH and it runs the same model almost as fast as as 32 core AMD at 3.7 GHz.

Your system is possibly too slow to saturate the 1080Ti at this small
system size. In a much larger system, the lead of the 1080 Ti over the
1080 may possibly reach the theoretical expectation.

> I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day in NPT.  And yes,  if you can send the pdb, top, and itps I’t would be interesting to compare the two AMDs.
> 

I did upload the stuff here + a readme-file. This system is much too
large for a single box + GPU (for productive runs), but maybe in 5 years
or so we can watch capillary waves through connected IMD/VMD in real-
time ;)

=> http://suwos.gibtsfei.net/d.dppc.4096.zip

Regards

Mirco