[gmx-users] How to make sure to reach the equalibrium state for the protein solution

[Tanping Li]

Dear David and all,

I have several questions when I solvate a protein in
water:

1. I follow the steps in manual: EM, restrain protein
MD and full MD. In this process, the Tem is increased
from intial 30K to final 300K. But I find that the
total potential also increases when Tem increase to
300K. Does this make sense?

2. I just follow the steps in manual, but I am not
sure if I reach to the real equilibrium state finally.
How to check it? This is the most important thing for
me now.

3. During the process, the LINCS WARNING occurs in the
initial procedures, I just decrease the timestep to
survive the MD. Is this correct?


Thank you very much. 

Best
Tanping