[AMBER] regarding remd

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Mon, 26 Jul 2010 15:29:31 +0200


I went through the tutorial for REMD and the article "Replica-exchange
molecular dynamics method for protein folding". After reading a couple of
article on the subject I am more confused about how to chose the temperature
distribution. In general it should be chosen geometrically and with the
degrees of freedom in mind - for the tutorial the following temperatures are

269.5, 300, 334, 371.8, 413.9, 460.7, 512.9,570.9

as I would like to try it on a couple of different peptides some of them
also have 272 degrees of freedom where I presume that the temperatures used
in the tutorial will be the same for those but others have more degrees of
freedom hence I would need to change the temperature to the corresponding
dof so could anyone guide me to where the calculations for the temperatures
are being performed?

I ran one of the simulation for 100 ns in implicit solvent and get
acceptance between the different intervals ranging form 0.17 to 0.19 which
seem that the detailed balance is fulfilled which I interpreted that the
temperature range for the 272 degrees of freedom is acceptable.
AMBER mailing list
Received on Mon Jul 26 2010 - 07:00:05 PDT
Custom Search