[gmx-users] How to set the temperatures for REMD?

[ZHANG Cheng]

My purpose of running REMD is to generate sufficient conformation sampling, and try to use them to explain the in vitro data at 65C (338.15K).


I am using the "Temperature generator for REMD-simulations" at http://folding.bmc.uu.se/remd/


I am not sure about the "standard/default" values of several parameters. Can I ask how to determine them?


1) Exchange probability: it should be a value between 0 to 1. The higher of the value I set, the shorter intervals of the temperatures are output. 


2) Tolerance: by default it is 1e-4. So I just use it?


3) Lower/Upper temperature limit: As I am interested in 338.15K, should the lower limit set to be 338.15K, while the upper limit as 373.15K (i.e.100C)? Should it be even higher?


4) Constraints in water: Fully flexible?


5) Constraints in the protein: All bonds?


6) Hydrogens in protein: All H? (what does this mean?)


Is there a general rule for the number of temperatures used in the REMD? Please feel free to tell me if there is a guidelines for setting the temperatures.


Thank you!