AMBER Archive (2006)

Subject: Re: AMBER: Replica Exchange

From: Austin B. Yongye (
Date: Fri Jul 21 2006 - 08:29:08 CDT

Thanks for the response.
I did contact the author of T-WHAM, but thought some AMBER users might
have used the code.
1. I used REMD because I thought I wasn't getting enough sampling from my
MD at room temperature.
2. Now that I have several trajectories after the REMD, I intend to
calculate rotamer populations of various dihedral angles in my molecules
to see if I am getting the correct experimental values. In this paper, J.
Am. Chem. Soc, 128, 5786-5791 (2006), the authors performed REMD and then
used T-WHAM for their population distribution analyses at room
I would like to do similar analysis.

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