Correct. Intrinsic radii only matter for implicit solvent simulations.
On Tue, Jun 1, 2010 at 12:21 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> 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
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>> --
>>>
>>> -----------------------------------------------------------------------------------
>>> 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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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -----------------------------------------------------------------------------------
> Dr. Dongshan Wei
> Department of Chemistry
> Boston University
> Boston, MA, 02215
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 01 2010 - 11:00:03 PDT
