Hello AMBER Users,
I am attempting to simulate the aggregation of surfactants in the presence
of various diamine counterions. These are the properties of my initial
"test" system that I am attempting to simulate:
- 20 mM surfactant concentration
- 250 surfactant units
- 250 counterion units
>From these parameters, I was able to determine that the appropriate
simulation box size required to hold 250 units while keeping a 20 mM
concentration is a (275 Angstrom)^3 box.
Further, calculating from the known density of the solution I am trying to
simulate (1.004 g/mL), I determined that 695K water molecules would need to
be added in order to reach experimental density in the (275 Angstrom)^3
box. This would be quite a bulky simulation that I would like to avoid if
possible.
>From a previous inquiry I made to this mailing list, I learned that
periodic boundaries are difficult (if not impossible) to implement into
implicit solvent simulations. However, I would like to find a way to
sidestep using this many water molecules if possible.
Additionally, if I were able to implement an implicit solvent into my
simulations, I was told that the lack of periodic boundaries would lead to
an "infinite" dilution which would lead to a loss of the intended 20 mM
surfactant concentration.
In summary, I would like to know how it would be possible to bypass using
so many water molecules in this situation. If implicit solvation is
possible, how could I implement distance restraints and/or periodic
boundaries so that I can still enforce the desired 20 mM surfactant
concentration in implicit solvent? Are there other workarounds for such
large systems that I am unaware of?
Any help is much appreciated.
Thanks so much,
NDB
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Received on Tue Mar 29 2022 - 10:00:03 PDT
