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From: Dongshan Wei <dswei0523.gmail.com>

Date: Tue, 1 Jun 2010 12:21:13 -0400

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
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Tue, 1 Jun 2010 12:21:13 -0400

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:

-- ----------------------------------------------------------------------------------- Dr. Dongshan Wei Department of Chemistry Boston University Boston, MA, 02215 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jun 01 2010 - 09:30:07 PDT

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