Hello experts:
I'm running a continuous constant pH MD using the GBNeck2-CPHMD simulation in Amber with replica exchange. In the AMBER manual, it says that first, the replica exchange log should be reformatted in a simpler form with the code walker_extraction, and after the output of this command is saved to a file, the ë files produced from the replica exchange simulation have to be sorted into new ë files containing the results from a single pH. This sorting is performed by the program wrap_traj. I don't know how to find these two codes: walker_extraction and wrap_traj. Does anyone know where they are located? Thank you very much for your help!
Best,
Nancy
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 26 2024 - 15:30:02 PDT
