[gmx-users] A question on REMD result analysis

[이종화]

Dear Gromacs users,

 

I’m trying to run a REMD simulation on a protein. After a lot of reading,
I am still unclear on the result analysis. Is it correct that, of many
replicas, I should select the frames from only the replica with my desired
temperature?(ex, room temp.) If not correct, how do I select the frames
from a REMD simulation as my final structures? If correct, should I ignore
some frames right after an exchange has occurred? I think they would not
have reached equilibrium and therefore not to be used.

 

I am quite confused. Any replies would be of great help.

 

Many thanks in advance,

 

John