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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Received on Tue Sep 03 2019 - 18:30:02 PDT
