note that the acceptance ratio doesn't imply detailed balance, and changes
to this only affect the efficiency, but not the actual results from long
simulations. Also note that the temperature RANGE can be important in
addition to the spacing.
Dan's suggestions for articles should help you optimize the efficiency of
your REMD simulations. This tutorial was about running REMD, so did not go
into depth on optimizing efficiency for different kinds of projects. Unless
a tutorial specifically says otherwise, you should assume it's designed to
get you started and may not always be the best choice of parameters, force
fields, simulation lengths and so on.
On Mon, Jul 26, 2010 at 9:29 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi,
>
> 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
> chosen:
>
> 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.
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Received on Mon Jul 26 2010 - 08:00:03 PDT
