Hi Jason,
Thanks so much for your reply which helps me make clear many questions.
But for the first question, If I do explicit solvent simulations, it's
not necessary to add "set default PBradii mbondi2" in the leap.in
script. Is it true?
Dongshan
On Mon, May 31, 2010 at 9:06 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
--
-----------------------------------------------------------------------------------
Dr. Dongshan Wei
Department of Chemistry
Boston University
Boston, MA, 02215
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Received on Tue Jun 01 2010 - 09:30:07 PDT
