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
>
>
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--
*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*
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Received on Thu Sep 12 2019 - 08:00:02 PDT
