Hello AMBER Users,
I have run into an issue while trying to create a simulation box containing
a random distribution of molecules (generated using Packmol). Each
individual unit has a floating-point value for its charge as reported in
LEaP, but I believe that the slight deviation from integral charge values
for each unit has conglomerated into a *very *non-integral charge for the
larger mixture.
Context: I plan on simulating surfactant aggregation in a system of 2500
anionic surfactants and 2500 organic diamine counterions. From known pKa
values and approximations of fraction ionized populations using the
Henderson-Hasselbach equation, I have determined that the system (at the
intended simulation pH) should consist of:
- 2500 anionic surfactants (Unit Name: UNAABC, -1 charge)
- 167 fully-protonated diamine counterions (Unit Name: AA2, +2 charge)
- 2305 partially-protonated diamine counterions (Unit Name: AA1, +1
charge)
- 28 fully-deprotonated diamine counterions (Unit Name: AA0, 0 charge)
- 139 Cl- ions to fully neutralize the solution (very loose
approximation of ionic contributions of water. Unit Name: Cl-, -1 charge)
When checking the charges of each residue in LEaP, I find that:
- UNA (Surfactant Tail, 0 Charge)
- "Total unperturbed charge: 0.000002, Total perturbed charge:
0.000002"
- ABC (Surfactant Head, -1 Charge)
- "Total unperturbed charge: -0.999998, Total perturbed charge:
-0.999998"
- AA2 (Fully-Protonated Diamine Counterion, +2 Charge)
- "Total unperturbed charge: 1.995998, Total perturbed
charge: 1.995998"
- AA1 (Partially-Protonated Diamine Counterion, +1 Charge)
- "Total unperturbed charge: 0.997999, Total perturbed charge:
0.997999"
- AA0 (Fully-Deprotonated Diamine Counterion, 0 Charge)
- "Total unperturbed charge: -0.000000, Total perturbed charge:
-0.000000"
However, when the mixture of these residues (2500 anionic surfactants, 2500
counterions in variety of protonation states) is created in Packmol and
loaded into LEaP, it has this to say about the charge: "Total unperturbed
charge: 133.724361, Total perturbed charge: 133.724361".
When adding the charges for each residue multiplied by how many of each
residue I added, I get roughly this number as well. However, this means
that I would not be able to add Cl- ions as intended to neutralize the
solution charge.
Does anyone have any suggested fixes for this? Any help is much appreciated.
All the best,
NDB
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Received on Sun Mar 13 2022 - 12:00:03 PDT
