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 Tue Sep 03 2019 - 19:00:02 PDT
