14. AMOEBA Plugin¶
OpenMM 7.7 provides a plugin that implements the AMOEBA polarizable atomic multipole force field from Jay Ponder’s lab. The AMOEBA force field may be used through OpenMM’s Python application layer. We have also created a modified version of TINKER (referred to as TINKER-OpenMM here) that uses OpenMM to accelerate AMOEBA simulations. TINKER-OpenMM can be created from a TINKER package using three files made available through the OpenMM home page. OpenMM AMOEBA Force and System objects containing AMOEBA forces can be serialized.
At present, AMOEBA is only supported on the CUDA and Reference platforms, not on the OpenCL platform.
In the following sections, the individual forces and options available in the plugin are listed, and the steps required to build and use the plugin and TINKER-OpenMM are outlined. Validation results are also reported. Benchmarks can be found on the OpenMM wiki at http://wiki.simtk.org/openmm/Benchmarks.
14.1. OpenMM AMOEBA Supported Forces and Options¶
14.1.1. Supported Forces and Options¶
The AMOEBA force terms implemented in OpenMM are listed in Table 14-1 along with the supported and unsupported options. TINKER options that are not supported for any OpenMM force include the grouping of atoms (e.g. protein chains), the infinite polymer check, and no exclusion of particles from energy/force calculations (‘active’/’inactive’ particles). The virial is not calculated for any force.
All rotation axis types are supported: ‘Z-then-X’, ‘Bisector’, ‘Z-Bisect’, ‘3-Fold’, ‘Z-Only’.
TINKER Force |
OpenMM Force |
Option/Note |
|---|---|---|
ebond1 (bondterm) |
AmoebaBondForce |
bndtyp=’HARMONIC’ supported, ‘MORSE’ not implemented |
Eangle71 (angleterm) |
AmoebaAngleForce |
angtyp=’HARMONIC’ and ‘IN-PLANE’ supported; ‘LINEAR’ and ‘FOURIER’ not implemented |
etors1a (torsionterm) |
PeriodicTorsionForce |
All options implemented; smoothing version(etors1b) not supported |
etortor1 (tortorterm) |
AmoebaTorsionTorsionForce |
All options implemented |
eopbend1 (opbendterm) |
AmoebaOutOfPlaneBendForce |
opbtyp = ‘ALLINGER’ implemented; ‘W-D-C’ not implemented |
epitors1 (pitorsterm) |
AmoebaPiTorsionForce |
All options implemented |
estrbnd1 (strbndterm) |
AmoebaStretchBendForce |
All options implemented |
ehal1a (vdwterm) |
AmoebaVdwForce |
ehal1b(LIGHTS) not supported |
empole1a (mpoleterm) |
AmoebaMultipoleForce |
poltyp = ‘MUTUAL’, ‘DIRECT’ supported |
empole1c (mpoleterm) PME |
AmoebaMultipoleForce |
poltyp = ‘MUTUAL’, ‘DIRECT’ supported; boundary= ‘VACUUM’ unsupported |
esolv1 (solvateterm) |
AmoebaWcaDispersionForce,
AmoebaGeneralizedKirkwoodForce
|
Only born-radius=’grycuk’ and solvate=’GK’ supported; unsupported solvate settings: ‘ASP’, ‘SASA’, ‘ONION’, ‘pb’, ‘GB-HPMF’, ‘Gk-HPMF’; SASA computation is based on ACE approximation |
eurey1 (ureyterm) |
HarmonicBondForce |
All options implemented |
Table 14-1: Mapping between TINKER and OpenMM AMOEBA forces
Some specific details to be aware of are the following:
Forces available in TINKER but not implemented in the OpenMM AMOEBA plugin include the following: angle-angle, out-of-plane distance, improper dihedral, improper torsion, stretch-torsion, charge-charge, atomwise charge-dipole, dipole-dipole, reaction field, ligand field, restraint, scf molecular orbital calculation; strictly speaking, these are not part of the AMOEBA force field.
Implicit solvent in TINKER-OpenMM is implemented with key file entry ‘solvate GK’. The entry ‘born-radius grycuk’ should also be included; only the ‘grycuk’ option for calculating the Born radii is available in the plugin.
In TINKER, the nonpolar cavity contribution to the solvation term is calculated using an algorithm that does not map well to GPUs. Instead the OpenMM plugin uses the TINKER version of the ACE approximation to estimate the cavity contribution to the SASA.
Calculations using the CUDA platform may be done in either single or double precision; for the Reference platform, double precision is used. TINKER uses double precision.
The TINKER parameter files for the AMOEBA force-field parameters are based on units of kilocalorie/Å, whereas OpenMM uses units of kilojoules/nanometer; both TINKER and OpenMM use picoseconds time units. Hence, in mapping the force-field parameters from TINKER files to OpenMM, many of the parameter values must be converted to the OpenMM units. The setup methods in the TINKER-OpenMM application perform the required conversions.
14.1.2. Supported Integrators¶
In addition to the limitations to the forces outlined above, TINKER-OpenMM can only use either the ‘Verlet’ or ‘Stochastic’ integrators when the OpenMM plugin is used; an equivalent to the TINKER ‘Beeman’ integrator is unavailable in OpenMM.
14.2. OpenMM AMOEBA Validation¶
OpenMM and TINKER 6.1.01 were each used to compute the atomic forces for dihydrofolate reductase (DHFR) in implicit and explicit solvent. Calculations used the CUDA platform, and were repeated for both single and double precision. For every atom, the relative difference between OpenMM and TINKER was computed as 2·|FMM–FT|/(|FMM|+|FT|), where FMM is the force computed by OpenMM and FT is the force computed by TINKER. The median over all atoms is shown in Table 14-2.
Because OpenMM and TINKER use different approximations to compute the cavity term, the differences in forces are much larger for implicit solvent than for explicit solvent. We therefore repeated the calculations, removing the cavity term. This yields much closer agreement between OpenMM and TINKER, demonstrating that the difference comes entirely from that one term.
Solvent Model |
single |
double |
|---|---|---|
Implicit |
1.04·10-2 |
1.04·10-2 |
Implicit (no cavity term) |
9.23·10-6 |
1.17·10-6 |
Explicit |
3.73·10-5 |
1.83·10-7 |
Table 14-2: Median relative difference in forces between OpenMM and TINKER
