Hello,
On Mon, May 31, 2010 at 3:04 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> Dear Carlos,
>
> Recently I'm beginning to learn REMD using Amber 10. I did the REMD
> tutorial, but I still have several questions about the tutorial.
>
> (1) What is the role of this line "set default PBradii mbondi2" in the
> leap.in script? If I do Ala10 explicit simulation, do I need to add
> this line in my leap.in script?
>
Different GB models use different sets of radii for the atoms. igb=5 and
igb=2 typically use the mbondi2 radii set, which is why this line is there.
I would add that line to your leap.in script if you plan to use one of those
implicit solvent models.
>
> (2) For T-REMD, how to correctly choose the starting temperature and
> end temperature? Is there a special sense to choose the starting
> temperature lower than 300K for peptide or protein systems?
>
>From what I understand, this is a large part of the "art" of running
successful REMD. Temperatures too high and you mostly sample ridiculous
regions of phase space that are irrelevant to room temperature.
Temperatures too low and you never jump barriers that you're looking to jump
in the first place. This is a non-answer born from not having run many REMD
simulations. What I would suggest, though, is to find some papers that use
REMD on systems similar to yours and see if their approach works for you
(regarding number of replicas and the temperature spacing between them).
Also, taken from the REMD tutorial:
... Typically the number of replicas would be related to the square root of
the number of atoms and the temperature distribution would be chosen to be a
geometric progression. There is much discussion in the literature about this
and you are advised to do a thorough literature search.
Usually REMD simulations are run for a temperature range between 270 - 600K.
Depending on your system a different temperature range may be required,
however, an in-depth discussion of this is beyond the scope of this
tutorial. We always need to have an even number of replicas since exchanges
are always attempted pair-wise...
>
> (3) The running average success rate is defined as
>
> successful swap times / (0.5* total attempt swap times)
>
> Is this definition is consistent with "acceptance ratio" which in
> most used in literature? I found in the literature there is no 0.5 in
> the denominator in the definition of the acceptance ratio.
>
This is also described in the tutorial: each swap attempt only occurs
between specific neighbors every other time (i.e. 1 attempts with 2 first,
the second time 2 attempts with 3). Therefore, the number of attempts
between a specific set of pairs is exactly half of the total number of
attempts made by one of the replicas. Hence the 0.5 factor. As worded in
the tutorial:
... we divide the # of successes by 0.5* the total attempts since each pair
is attempted only every other exchange), ...
All the best,
Jason
> Thanks so much for your time!
>
> Dongshan
>
>
> On Mon, Mar 29, 2010 at 8:02 AM, Carlos Simmerling
> <carlos.simmerling.gmail.com> wrote:
> > the need for this depends on the highest temperature you are going to
> use.
> > at 400K I think these problems are very unlikely. personally I do not
> > benefit from going to higher than 400K. if you do, such as 600-700K, then
> > you really need to use restraints. you might need to make your own script
> to
> > create them.
> >
> > On Mon, Mar 29, 2010 at 7:49 AM, maya maya <harish.maya83.gmail.com>
> wrote:
> >
> >> DEAR AMBER !
> >>
> >> I have seen the REMD tutorial , i have a doubt regarding the step
> >>
> >> $AMBERHOME/exe/makeCHIR_RST ala10.pdb
> >> ala10_chir.dat<
> >> http://ambermd.org/tutorials/advanced/tutorial7/files/ala10_chir.dat>
> >>
> >> which has been given in the tutorial . It is meant for proteins, but if
> one
> >> would like to REMD for DNA
> >> how to make this .
> >>
> >> If any one can give example , it will be better for my understanding .
> >>
> >>
> >> regards
> >> maya
> >> _______________________________________________
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> >>
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> >
>
>
>
> --
>
> -----------------------------------------------------------------------------------
> Dr. Dongshan Wei
> Department of Chemistry
> Boston University
> Boston, MA, 02215
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 31 2010 - 18:30:03 PDT
