[gmx-users] Performance drops when simulating protein with small ligands

[Yunlong Liu]

Hi,

I am running my protein with two ligands. Both ligands are small 
molecules like ATP. However, my simulation performance drops a lot by 
adding this two ligands with the same set of other parameters.

Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But 
now I can only gain 17 ns/day with the same setting. I want to know 
whether this is a common phenomenon or I do something stupid.

Yunlong