
README for the AA_inner-ion_Wanes26.v1 force field (4/07/2026).

Authors:
George Wanes (wanes.g@northeastern.edu)
Paul Whitford (p.whitford@northeastern.edu)

Included Files:
AA_inner-ion_Wanes26.v1.b 
AA_inner-ion_Wanes26.v1.bif
AA_inner-ion_Wanes26.v1.nb
AA_inner-ion_Wanes26.v1.sif
AA_inner-ion_Wanes26.v1.extras  
AA_inner-ion_Wanes26.v1.ions.def (for use with smog_ion)  
AA_inner-ion_Wanes26.v1.map (for use with smog_adjustPDB)


General description:
This model is an all-atom model with bonded geometry (bond lengths and angles) defined based on the AMBER force field and effective nonbonded ion-ion, ion-biomolecule potentials are included. Excluded volume terms are either from comparison with AMBER, or refinement against explicit-solvent simulations. 


For a detailed description of the model, see: 
Wanes G, Mohanty U and Whitford PC
Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.
Proceedings of the National Academy of Sciences USA (2026)
DOI: 10.1073/pnas.2527693123 


Model Resolution:
All non-H atoms are explicitly represented in RNA and proteins.  Ions are explicitly included.  Water  molecules are not included.


New features introduced in this model (described in Wanes et al, 2026): 
For ion-ion and ion-polymer interactions, the potential (in addition to the Coulomb term) is defined by 1/r^12 + 7 Gaussians.  The functional form of the potential was adopted based on the works of Savelyev and Papoian (J Chem Phys B, 113, 7786-93, 2009), though the current parameters were developed subsequently (described in Wanes et al. 2026) for this all-atom model. This model differs from that of Wang et al (2022), in that the previous model only included diffuse ions (i.e. 5 Gaussians), whereas this model also includes inner-shell ions (7 Gaussians).


Supported residues and atoms:
Standard protein and RNA residues.  See .map file for full list of supported residues.
K+, Cl- and Mg2+


Aspects built upon earlier models:
The distributions of stabilizing energetic terms (i.e. dihedrals vs. contacts) were assigned consistent with Whitford et al, Proteins (2009) and Noel et al. PLOS Comp Bio (2016). 

The contact map is based on the Shadow Contact Map algorithm (Noel, et al. JCP 2012) with a 6A cutoff with 1A atom radius.

The minimum for each contact is positioned at 0.96 times the native distance.  This was first introduced in simulations of the ribosome (Nguyen and Whitford, Nature Comm, 2016) to avoid artificial expansion. That is, the SMOG model defines the potential energy minimum. If native distances are used, then the free-energy minimum is slightly expanded, due to entropic contributions. We have found that, generally, scaling by 0.96 ensures that the native distance is very close to the free-energy minimum (at T=0.5 reduced units).

The bond lengths and distances are assigned the values given in the AMBER FF03 force field (Duan, et al. JCC 2003), as employed in a previous AMBER-SMOG model (Whitford, et al. Viruses 2020. SMOG 2 Force Field Repo ID: SBM_AA-amber-bonds). Similarly, planar dihedrals are assigned cosine potentials with periodicity 2. 

Described in Wang et al, JACS 2022: Non-bonded (vdW-like) interactions are assigned an 18-12 interaction, with parameters that were based on fitting to the 12-6 parameters of the AMBER FF03 force field.  Fitting was applied so that the excluded-volume of each atom mimics the AMBER excluded volume, while introducing a near-zero-depth attractive well.

Described in Wang et al, JACS 2022: Partial charges are assigned to each non-H atom using a unified-atom charge representation, where H charges are consolidated on their respective non-H atoms. A Coulomb potential was used for all charge-charge interactions. In this model, the effective potentials were parameterized to a temperature of 0.5 (reduced units), or 60 in Gromacs units.  Since this temperature is intended to model room temperature (T=300K), the scale of the electrostatic interactions needs to be reduced by a factor of 5. When using Gromacs, this is accomplished by increasing the dielectric constant to 400 (instead of 80 for water). When using OpenSMOG/OpenMM, then the rescaling is already encoded in the template files, and no additional changes are required by the user.


Version Information:
These templates are only compatible with SMOG 2, version 2.4.4 and later. It's always recommended that one uses the newest version of SMOG 2.


OpenMM Usage: This force field may be used with the -OpenSMOG flag in SMOG 2, which are compatible with OpenSMOG (v1.1 or later). It is always recommended that one uses the newest version of OpenSMOG.


Gromacs Usage: This model is not supported by Gromacs.


Other usage Notes:
	When adding ions with smog_ion, make sure to use the -t flag and give this template directory name, so that the proper names of charges will be given.


Sample Usage:
Input decks, including Python-based OpenSMOG scripts, are available at https://github.com/Whitford/SMOGionSimulations, which is archived on zenodo (DOI:10.5281/zenodo.19081083)



