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?
(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?
(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.
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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Received on Mon May 31 2010 - 12:30:04 PDT
