Dongshan,
I had the same issues as you with Chodera code, but eventually got numpy
and scipy installed.
Regardless, building your own code may be worth it.
>
> (1) How to determine the energy bin? Here the energy is total energy
> or just potential energy in temperature REMD? In order to get the
> energy distribution, whether or not are all of the energies from
> different temperatures and different replicas counted?
>
> You can use the potential energy. You definitely need information from all
temperatures.
> (2) To read the energy values from T-REMD simulations, should I read
> them from .mden file or .mdout file? Both of these two files records
> the energy values at each interval of ntwr and ntpr. In addition, I
> found the temperature for each replica at the same simulation time in
> .mdcrd file and in .mdout is the same, but is different from any value
> of Temp, T_solute, T_solv in .mden file. Why is there difference of
> the recorded temperature in .mden and .mdout files?
>
> As long as it has the correct potential energy, either one is fine. I
usually use
the rem.log since it is very easy to sort things by temperature or replica
index. Note,
if you attempt exchanges infrequently, the rem.log won't have as many data
points.
In general, I use the target temperature, rather than the instantaneous
temperature.
> (3) About the equation of g=1+2*tau, is it safe to simplify g=1? How
> do you determine the correlation time tau and what is the magnitude in
> order of tau for small biological system (one peptide chain and ~1000
> TIP4P water)?
>
I think John Chodera's code calculates the autocorrelation time within the
code. The shortcut
is to take data points every x time steps. Assuming that x is around the
autocorrelation
time, you can assume g=1. I think you can probably get less error by
calculating each
tau, but I'm lazy. If it's in solvent, it may be safe to look up the
autocorrelation time of your
particular solvent (since it dominates the energy). If you exchange quite
often, I believe
the autocorrelation time should decrease.
-Dan
Thanks so much for time!
>
> Best!
>
> Dongshan
>
> On Tue, Jul 27, 2010 at 7:34 AM, Daniel Sindhikara <sindhikara.gmail.com>
> wrote:
> > Carlos,
> > The Chodera code is specifically made for T-WHAM. Alan Grossfield has
> > implemented
> > T-WHAM a year or two ago. HOWEVER, I had problems with its numerical
> > stability for T-WHAM.
> > I believe this is because it handles the DOS in normal space rather than
> log
> > space (last I checked).
> > --Dan
> >
> > On Tue, Jul 27, 2010 at 8:18 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> do those codes do T-WHAM?
> >>
> >> On Tue, Jul 27, 2010 at 7:15 AM, Daniel Sindhikara <
> sindhikara.gmail.com
> >> >wrote:
> >>
> >> > Dongshan,
> >> > You can either develop your own code, or use someone else's such as:
> >> > Alan Grossfields: http://membrane.urmc.rochester.edu/content/wham
> >> > or
> >> > John Chodera's: http://www.dillgroup.ucsf.edu/~jchodera/code/WHAM/<http://www.dillgroup.ucsf.edu/%7Ejchodera/code/WHAM/>
> <http://www.dillgroup.ucsf.edu/%7Ejchodera/code/WHAM/>
> >> <http://www.dillgroup.ucsf.edu/%7Ejchodera/code/WHAM/>
> >> >
> >> > Someone else might have a "more straightforward" way of doing this.
> >> > I use my own code, but in its current condition I couldn't lend it out
> >> > *yet*in
> >> > full conscience. :P
> >> > --Dan
> >> >
> >> >
> >> > On Tue, Jul 27, 2010 at 7:43 AM, Dongshan Wei <dswei0523.gmail.com>
> >> wrote:
> >> >
> >> > > Hi Everyone,
> >> > >
> >> > > Recently I want to do a ramachandran plot for an Alanine peptide. I
> >> > > did a 10ns temperature REMD simulations with 16 replicas. Now I want
> >> > > to weight the probability for temperatures not at T0 to get the
> >> > > weighted ramachandran plot. I made a quick look through the mailing
> >> > > list and find most WHAM is combined with umbrella sampling. Can
> >> > > somebody give a clear procedure on how to do WHAM based on REMD
> >> > > simulations outputs?
> >> > >
> >> > > Thanks so much!
> >> > >
> >> > > Dongshan
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
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> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Dr. Daniel J. Sindhikara
> >> > Institute for Molecular Science
> >> > E-mail: sindhikara.gmail.com
> >> > Website: http://sites.google.com/site/dansindhikara/
> >> > --
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
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> >> >
> >> _______________________________________________
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> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
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>
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Sun Aug 01 2010 - 21:30:03 PDT
