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 - 07:30:02 PDT
