By quirks I mean:
how to relax the system (NPT, NVT, NVE)
what cutoff to use
what force fields to use
How long does it takes to get converged observables in a medium with
high viscosity, etc
Nothing that cannot be learned from doing the explicit solvent
tutorials, and doing your own system in regular MD before trying REMD.
Adrian
On 6/8/11 10:55 AM, mish wrote:
> Hello Dr. Adrian:
> Thanks a lot. Yes noticed it now that simulations are dune using generalized
> Born implicit solvent. I am basically trying the folding of
> oligo-saccharides. In my opinion, the case of saccharides hydrogen bonding
> (water and -OH from sugar) could be of really importance and thats why I
> want to try REMD in explicit solvent. Could you please elaborate if you mean
> any particular "quircks of explicit solvent MD" ?
>
>
>
> Sincerely
> Mish
>
>
> On Wed, Jun 8, 2011 at 10:28 AM, Adrian Roitberg<roitberg.qtp.ufl.edu>wrote:
>
>> Dear Mish
>>
>> First, the tutorial is NOT in vacuum, it is in implicit solvent (igb=5).
>>
>> Second, for explicit solvent REMD you want the same cutoff as you would
>> use for explicit solvent regular MD. Just make sure you are familiar
>> with the quircks of explicit solvent MD before trying to go into REMD.
>>
>> Adrian
>>
>>
>> On 6/8/11 10:20 AM, mish wrote:
>>> Hi:
>>> A short question related to tutorial 7 " Replica Exchange Simulations
>> with
>>> AMBER 10" in the amber website. Authors use no cut off for simulation in
>>> vacuum. What about the non-bonded cutoff in the case of REMD in explicit
>>> solvent ?
>>>
>>> Sincerely
>>> Mish*
>>> *
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>>
>> on Sabbatical in Barcelona until August 2011.
>> Email roitberg.ufl.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Jun 08 2011 - 03:30:04 PDT
