For large systems, explicit solvent may be faster than implicit. But a
bigger question may be about the system boundary - will your system behave
properly if there is no periodic boundary? I don't think that there is
support to maintain your cubic system geometry in implicit solvent unless
you add some type of restraints. Since there is no defined volume, the
system is infinitely dilute and will no longer correspond to 60 mM.
On Mon, Mar 21, 2022, 7:28 AM Nathan Black <nathanblack262.gmail.com> wrote:
> Hello AMBER Users,
>
> I am attempting to simulate a very large system (2500 anionic surfactants
> and 2500 organic counterions, a grand total of ~150K atoms) in a (245
> Angstrom)^3 cubic region to approximate a 60 mM surfactant solution, as
> defined in Packmol.
>
> My purpose in doing this is to model aggregation behavior- as some
> surfactant micelles related to mine are known to have aggregation numbers
> (N) in the 300-400 range, I wanted to add a larger number of surfactants so
> that (assuming some degree of adherence to experimental findings) multiple
> micelles would form in each simulation.
>
> To reduce the computational expense of a simulation for this large system,
> I attempted to set a nonbonded interaction cutoff of 10.0 Angstroms (cut =
> 10.0), choose a Generalized Born implicit solvation model (igb = 5), and
> run using GPUs (implementation with pmemd.cuda). However, I received an
> error message when attempting this simulation- I did some further digging
> and found that the nonbonded interaction cutoff must be set to the system
> size when igb > 0 while using pmemd.cuda.
>
> I will experiment with reducing the size of the system, but are there any
> known workarounds to this? I ask that question knowing that this design was
> probably intentional.
>
> I understand that it is good practice to set a large cutoff when working
> with implicit solvent, but at this point the simulations would run for far
> too long to be useful, given that my system (the minimization of one such
> 60 mM surfactant "solution" took about 24 hours when run on CPUs with cut =
> 10.0) is incredibly large.
>
> Let me know if there is any other information I can give to help answer my
> question. Any help is much appreciated.
>
> Thanks so much,
> NDB
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Received on Mon Mar 21 2022 - 11:00:02 PDT
