Hi
I have been looking at the suggested articles. In my case I use an implicit
solvent and have been looking at the Met-Enkephalin simulation by Sugita &
Okamoto.
So as I understand the Tmin and Tmax - the minimum could be the biological
relevant and Tmax should be able to overcome large energy barriers around
500 - 650 K is suggested. I do not after reading the articles find some
specific value which probably indicates that ones has to be sure that the
system is ergodic. Again I look for acceptance which should be around
0.15-0.20 - empirical value.
So for the calculation I find the following expressions in Fukunishi et al.
Tm ~ T0*exp(m/sqrt(dof))
with M number of replica given as
M ~ sqrt(f) * ln(Tmax/Tmin)
For the minimum temperature I have not been able to find some good
discussion on it - should it be lower than my "wanted" temperature of 300 K
or should that be the lowest one? Does some of this make sense at all? :-)
On Mon, Jul 26, 2010 at 4:44 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 13:00:04 PDT
