GPU computing is slow

[chenshixinnb]

Same multimer sequence,two chains,in total 646AA.

Use ParallelFold,CPU phase use 1h33min,GPU phase use 5h30min,generate five models.command: -p multimer -m model_1_multimer,model_2_multimer,model_3_multimer,model_4_multimer,model_5_multimer.

Use ParallelFold,CPU phase use 1h27min,GPU phase use 1h25min,generate one models.command: -p multimer -m model_1_multimer

Use Alphafold Docker,total use 2h20min,generate five models

[Zuricho]

When using multimer models, sometimes a collapsed structure may cause the running time and amber relaxation time very long.
Did you look into the predicted computed structure? Is it correct or reasonable?

[chenshixinnb]

How can I determine if the calculation structure is reasonable?Do you have any relevant references?
Thanks.

[Zuricho]

you can just look at the output structure, is it looked reasonable? like does it have reasonable secondary structure?
also, you can check which step took longest time? is it inference or relaxation?