Thanks for the valuable comments. I find that, they are faster, can be
useful at situations, where explicit details of the solvents can be
neglected
Santo
On Fri, 13 Sep 2019 at 09:14, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> I agree with Matias about the misconception, MD is not always faster in GB-
> it can actually take more computer resources per time stepas discussed in
> the links he provided . However it can parallelize better, and some global
> motions may be sampled in many fewer steps than corresponding dynamics in
> explicit solvent. My view is that these are two different models, each with
> their own strengths and weaknesses. One is not "better" than the other. For
> some projects one is the right choice, for other projects it is not. There
> is always a tradeoff between precision and accuracy. One must be aware of
> the limitations of all of our models and choose the appropriate one.
> Another good example is QM vs MM - each is the appropriate tool in a
> different situation.
> Carlos
>
> On Thu, Sep 12, 2019 at 10:38 AM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Just a follow up comment to David's...
> >
> > There seems to be a general misconception about the speedup of implicit
> > solvent simulations... most people believe they are faster that explicit
> > ones just because there is no water molecules, but they usually neglect
> > several other issues of implementation and so on...
> >
> > I recommend you to read these two previous threats on the topic:
> >
> > + http://archive.ambermd.org/201807/0309.html
> > + http://archive.ambermd.org/201806/0279.html
> >
> > Another advice for free... sometime you do need explicit solvent
> > (water/ions) to correctly describe an interaction or phenomenon and there
> > is no workaround for that... so, if someone wants to sell you a Ferrari
> for
> > a dollar, then be suspicious...
> >
> > Best,
> >
> > MatÃas
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "Kolattukudy P. Santo" <santotheophys.gmail.com>
> > Para: "David Case" <david.case.rutgers.edu>, "AMBER Mailing List" <
> > amber.ambermd.org>
> > Enviados: Martes, 3 de Septiembre 2019 22:45:42
> > Asunto: Re: [AMBER] GBSA
> >
> > Thank you, Dave for the answers
> > Regards
> > Santo
> >
> > On Tue, 3 Sep 2019 at 21:19, David Case <david.case.rutgers.edu> wrote:
> >
> > > On Tue, Sep 03, 2019, Kolattukudy P. Santo wrote:
> > >
> > > >I am trying to do implicit solvent simulations in AMBER, with
> > generalized
> > > >Born solvation. (1) Is it really faster than explicit MD? ( I dont
> find
> > it
> > > >is that faster !).
> > >
> > > It is often the case that explicit solvent simualtions (which take
> > > advantage of PME to handle long-range electrostatic interactions) can
> be
> > > faster than the corresponding implicit solvent simulations (which don't
> > > make use of PME). Balancing off against this is that, generally,
> > > conformational exploration is faster in implicit solvents, so you
> should
> > > not just look at ns/day as the only metric.
> > >
> > >
> > > (2) Is it appropriate for simulating very long polymers, say
> > > >with 100 or more monomers ?
> > >
> > > Sure.....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > *Dr. K. P. Santo*
> > *Post doctoral Associate *
> > *Department of Chemical and Biochemical Engineering*
> > *Rutgers, The State University of New Jersey*
> > *New Brunswick, New jersey*
> > *USA*
> > _______________________________________________
> > 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
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Kolattukudy P. Santo*
*Post doctoral Associate *
*Department of Chemical and Biochemical Engineering*
*Rutgers, The State University of New Jersey*
*New Brunswick, New jersey*
*USA*
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Received on Fri Sep 13 2019 - 08:00:02 PDT
