[gmx-users] Replica exchange question?

Hanin Omar hanin_omar85 at yahoo.com
Mon Apr 22 13:52:46 CEST 2019

Hello all;i want to perform a REMD simulation with orientation restraint added, and i want to make sure that my scheme is correct so i have a few questions:1)  if i have dihedral restraint or/and orientation restraint they should be added in all steps ( energy minimization, temperature coupling, pressure coupling and md production) right?2) when i do REMD, i perform temperature equiliberation for the different replicas at different temperature, following that i perform pressure equilibration at the same pressure values for all replica, then i run the replica exchange production, is that correct?3) is 500 exchange rate a good value for a 83 residue helical protein?4) i am confused, does REMD produces a different trajectory for each replica, because each replica has a slightly different md.log file? if so which replica should i consider the final best result?i really appreciate the helpHanin OMar

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