[gmx-users] How to make sure to reach the equalibrium state for the protein solution
jia_11_osu at yahoo.com
Fri Jul 29 23:50:31 CEST 2005
Dear David and all,
I have several questions when I solvate a protein in
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
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.
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