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
>
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>
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Received on Wed Jun 08 2011 - 02:00:02 PDT
