Examples with Crystal ffx.crystal.Crystal used on opensource projects

Example 16 with Crystal

use of ffx.crystal.Crystal in project ffx by mjschnie.

the class XYZFilter method readPBC.

/**
 * Attempt to parse the String as unit cell parameters.
 *
 * @param data The String to parse.
 *
 * @return false if the first token in the String is an integer and true
 * otherwise.
 */
private static boolean readPBC(String data, MolecularAssembly activeMolecularAssembly) {
    if (firstTokenIsInteger(data)) {
        return false;
    }
    String[] tokens = data.trim().split(" +");
    if (tokens != null && tokens.length == 6) {
        CompositeConfiguration config = activeMolecularAssembly.getProperties();
        double a = Double.parseDouble(tokens[0]);
        double b = Double.parseDouble(tokens[1]);
        double c = Double.parseDouble(tokens[2]);
        double alpha = Double.parseDouble(tokens[3]);
        double beta = Double.parseDouble(tokens[4]);
        double gamma = Double.parseDouble(tokens[5]);
        config.setProperty("a-axis", a);
        config.setProperty("b-axis", b);
        config.setProperty("c-axis", c);
        config.setProperty("alpha", alpha);
        config.setProperty("beta", beta);
        config.setProperty("gamma", gamma);
        Crystal crystal = activeMolecularAssembly.getCrystal();
        if (crystal != null) {
            crystal.changeUnitCellParameters(a, b, c, alpha, beta, gamma);
        }
    }
    return true;
}

Example 17 with Crystal

use of ffx.crystal.Crystal in project ffx by mjschnie.

the class XYZFilter method writeFile.

/**
 * {@inheritDoc}
 */
@Override
public boolean writeFile(File saveFile, boolean append) {
    if (saveFile == null) {
        return false;
    }
    try {
        File newFile = saveFile;
        if (!append) {
            newFile = version(saveFile);
        }
        activeMolecularAssembly.setFile(newFile);
        activeMolecularAssembly.setName(newFile.getName());
        FileWriter fw;
        if (append && !newFile.exists()) {
            fw = new FileWriter(newFile);
        } else {
            fw = new FileWriter(newFile, append);
        }
        BufferedWriter bw = new BufferedWriter(fw);
        // XYZ File First Line
        int numberOfAtoms = activeMolecularAssembly.getAtomList().size();
        String output = format("%7d  %s\n", numberOfAtoms, activeMolecularAssembly.toString());
        bw.write(output);
        Crystal crystal = activeMolecularAssembly.getCrystal();
        if (!crystal.aperiodic()) {
            Crystal uc = crystal.getUnitCell();
            String params = String.format("%14.8f%14.8f%14.8f%14.8f%14.8f%14.8f\n", uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
            bw.write(params);
        }
        Atom a2;
        StringBuilder line;
        StringBuilder[] lines = new StringBuilder[numberOfAtoms];
        // XYZ File Atom Lines
        ArrayList<Atom> atoms = activeMolecularAssembly.getAtomList();
        Vector3d offset = activeMolecularAssembly.getOffset();
        for (Atom a : atoms) {
            if (vdwH) {
                line = new StringBuilder(String.format("%7d %3s%14.8f%14.8f%14.8f%6d", a.getIndex(), a.getAtomType().name, a.getRedX() - offset.x, a.getRedY() - offset.y, a.getRedZ() - offset.z, a.getType()));
            } else {
                line = new StringBuilder(String.format("%7d %3s%14.8f%14.8f%14.8f%6d", a.getIndex(), a.getAtomType().name, a.getX() - offset.x, a.getY() - offset.y, a.getZ() - offset.z, a.getType()));
            }
            for (Bond b : a.getBonds()) {
                a2 = b.get1_2(a);
                line.append(format("%8d", a2.getIndex()));
            }
            lines[a.getIndex() - 1] = line.append("\n");
        }
        try {
            for (int i = 0; i < numberOfAtoms; i++) {
                bw.write(lines[i].toString());
            }
        } catch (IOException e) {
            String message = format(" Their was an unexpected error writing to %s.", getActiveMolecularSystem().toString());
            logger.log(Level.WARNING, message, e);
            return false;
        }
        bw.close();
        fw.close();
    } catch (IOException e) {
        String message = format(" Their was an unexpected error writing to %s.", getActiveMolecularSystem().toString());
        logger.log(Level.WARNING, message, e);
        return false;
    }
    return true;
}

Example 18 with Crystal

use of ffx.crystal.Crystal in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addAmoebaMultipoleForce.

private void addAmoebaMultipoleForce() {
    ParticleMeshEwald pme = super.getPmeNode();
    if (pme == null) {
        return;
    }
    int[][] axisAtom = pme.getAxisAtoms();
    double dipoleConversion = OpenMM_NmPerAngstrom;
    double quadrupoleConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double polarityConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double dampingFactorConversion = sqrt(OpenMM_NmPerAngstrom);
    amoebaMultipoleForce = OpenMM_AmoebaMultipoleForce_create();
    double polarScale = 1.0;
    if (pme.getPolarizationType() != Polarization.MUTUAL) {
        OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Direct);
        if (pme.getPolarizationType() == Polarization.NONE) {
            polarScale = 0.0;
        }
    } else {
        ForceField forceField = molecularAssembly.getForceField();
        String algorithm = forceField.getString(ForceField.ForceFieldString.SCF_ALGORITHM, "CG");
        ParticleMeshEwald.SCFAlgorithm scfAlgorithm;
        try {
            algorithm = algorithm.replaceAll("-", "_").toUpperCase();
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.valueOf(algorithm);
        } catch (Exception e) {
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.CG;
        }
        switch(scfAlgorithm) {
            case EPT:
                logger.info(" Using extrapolated perturbation theory approximation instead of full SCF calculations. Not supported in FFX reference implementation.");
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Extrapolated);
                PointerByReference exptCoefficients = OpenMM_DoubleArray_create(4);
                OpenMM_DoubleArray_set(exptCoefficients, 0, -0.154);
                OpenMM_DoubleArray_set(exptCoefficients, 1, 0.017);
                OpenMM_DoubleArray_set(exptCoefficients, 2, 0.657);
                OpenMM_DoubleArray_set(exptCoefficients, 3, 0.475);
                OpenMM_AmoebaMultipoleForce_setExtrapolationCoefficients(amoebaMultipoleForce, exptCoefficients);
                OpenMM_DoubleArray_destroy(exptCoefficients);
                break;
            case CG:
            case SOR:
            default:
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Mutual);
                break;
        }
    }
    PointerByReference dipoles = OpenMM_DoubleArray_create(3);
    PointerByReference quadrupoles = OpenMM_DoubleArray_create(9);
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        MultipoleType multipoleType = atom.getMultipoleType();
        PolarizeType polarType = atom.getPolarizeType();
        /**
         * Define the frame definition.
         */
        int axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
        switch(multipoleType.frameDefinition) {
            case ZONLY:
                axisType = OpenMM_AmoebaMultipoleForce_ZOnly;
                break;
            case ZTHENX:
                axisType = OpenMM_AmoebaMultipoleForce_ZThenX;
                break;
            case BISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_Bisector;
                break;
            case ZTHENBISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ZBisect;
                break;
            case TRISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ThreeFold;
                break;
            default:
                break;
        }
        double useFactor = 1.0;
        if (!atoms[i].getUse() || !atoms[i].getElectrostatics()) {
            // if (!atoms[i].getUse()) {
            useFactor = 0.0;
        }
        // Should be 1.0 at this point.
        double lambdaScale = lambda;
        if (!atom.applyLambda()) {
            lambdaScale = 1.0;
        }
        useFactor *= lambdaScale;
        /**
         * Load local multipole coefficients.
         */
        for (int j = 0; j < 3; j++) {
            OpenMM_DoubleArray_set(dipoles, j, multipoleType.dipole[j] * dipoleConversion * useFactor);
        }
        int l = 0;
        for (int j = 0; j < 3; j++) {
            for (int k = 0; k < 3; k++) {
                OpenMM_DoubleArray_set(quadrupoles, l++, multipoleType.quadrupole[j][k] * quadrupoleConversion * useFactor / 3.0);
            }
        }
        // int zaxis = 0;
        int zaxis = 1;
        // int xaxis = 0;
        int xaxis = 1;
        // int yaxis = 0;
        int yaxis = 1;
        int[] refAtoms = axisAtom[i];
        if (refAtoms != null) {
            zaxis = refAtoms[0];
            if (refAtoms.length > 1) {
                xaxis = refAtoms[1];
                if (refAtoms.length > 2) {
                    yaxis = refAtoms[2];
                }
            }
        } else {
            axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
            logger.info(String.format(" Atom type %s", atom.getAtomType().toString()));
        }
        double charge = multipoleType.charge * useFactor;
        /**
         * Add the multipole.
         */
        OpenMM_AmoebaMultipoleForce_addMultipole(amoebaMultipoleForce, charge, dipoles, quadrupoles, axisType, zaxis, xaxis, yaxis, polarType.thole, polarType.pdamp * dampingFactorConversion, polarType.polarizability * polarityConversion * polarScale);
    }
    OpenMM_DoubleArray_destroy(dipoles);
    OpenMM_DoubleArray_destroy(quadrupoles);
    Crystal crystal = super.getCrystal();
    if (!crystal.aperiodic()) {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_PME);
        OpenMM_AmoebaMultipoleForce_setCutoffDistance(amoebaMultipoleForce, pme.getEwaldCutoff() * OpenMM_NmPerAngstrom);
        OpenMM_AmoebaMultipoleForce_setAEwald(amoebaMultipoleForce, pme.getEwaldCoefficient() / OpenMM_NmPerAngstrom);
        double ewaldTolerance = 1.0e-04;
        OpenMM_AmoebaMultipoleForce_setEwaldErrorTolerance(amoebaMultipoleForce, ewaldTolerance);
        PointerByReference gridDimensions = OpenMM_IntArray_create(3);
        ReciprocalSpace recip = pme.getReciprocalSpace();
        OpenMM_IntArray_set(gridDimensions, 0, recip.getXDim());
        OpenMM_IntArray_set(gridDimensions, 1, recip.getYDim());
        OpenMM_IntArray_set(gridDimensions, 2, recip.getZDim());
        OpenMM_AmoebaMultipoleForce_setPmeGridDimensions(amoebaMultipoleForce, gridDimensions);
        OpenMM_IntArray_destroy(gridDimensions);
    } else {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_NoCutoff);
    }
    OpenMM_AmoebaMultipoleForce_setMutualInducedMaxIterations(amoebaMultipoleForce, 500);
    OpenMM_AmoebaMultipoleForce_setMutualInducedTargetEpsilon(amoebaMultipoleForce, pme.getPolarEps());
    int[][] ip11 = pme.getPolarization11();
    int[][] ip12 = pme.getPolarization12();
    int[][] ip13 = pme.getPolarization13();
    ArrayList<Integer> list12 = new ArrayList<>();
    ArrayList<Integer> list13 = new ArrayList<>();
    ArrayList<Integer> list14 = new ArrayList<>();
    PointerByReference covalentMap = OpenMM_IntArray_create(0);
    for (int i = 0; i < nAtoms; i++) {
        Atom ai = atoms[i];
        list12.clear();
        list13.clear();
        list14.clear();
        for (Bond bond : ai.getBonds()) {
            int index = bond.get1_2(ai).getIndex() - 1;
            OpenMM_IntArray_append(covalentMap, index);
            list12.add(index);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent12, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Angle angle : ai.getAngles()) {
            Atom ak = angle.get1_3(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index)) {
                    list13.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent13, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Torsion torsion : ai.getTorsions()) {
            Atom ak = torsion.get1_4(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index) && !list13.contains(index)) {
                    list14.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent14, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Atom ak : ai.get1_5s()) {
            int index = ak.getIndex() - 1;
            if (!list12.contains(index) && !list13.contains(index) && !list14.contains(index)) {
                OpenMM_IntArray_append(covalentMap, index);
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent15, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (int j = 0; j < ip11[i].length; j++) {
            OpenMM_IntArray_append(covalentMap, ip11[i][j]);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_PolarizationCovalent11, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
    // for (int j = 0; j < ip12[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip12[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent12, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // for (int j = 0; j < ip13[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip13[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent13, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent14, covalentMap);
    }
    OpenMM_IntArray_destroy(covalentMap);
    OpenMM_System_addForce(system, amoebaMultipoleForce);
    OpenMM_Force_setForceGroup(amoebaMultipoleForce, 1);
    logger.log(Level.INFO, " Added polarizable multipole force.");
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        addGKForce();
    }
}

Example 19 with Crystal

use of ffx.crystal.Crystal in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method setDefaultPeriodicBoxVectors.

private void setDefaultPeriodicBoxVectors() {
    OpenMM_Vec3 a = new OpenMM_Vec3();
    OpenMM_Vec3 b = new OpenMM_Vec3();
    OpenMM_Vec3 c = new OpenMM_Vec3();
    Crystal crystal = super.getCrystal();
    if (!crystal.aperiodic()) {
        a.x = crystal.a * OpenMM_NmPerAngstrom;
        a.y = 0.0 * OpenMM_NmPerAngstrom;
        a.z = 0.0 * OpenMM_NmPerAngstrom;
        b.x = 0.0 * OpenMM_NmPerAngstrom;
        b.y = crystal.b * OpenMM_NmPerAngstrom;
        b.z = 0.0 * OpenMM_NmPerAngstrom;
        c.x = 0.0 * OpenMM_NmPerAngstrom;
        c.y = 0.0 * OpenMM_NmPerAngstrom;
        c.z = crystal.c * OpenMM_NmPerAngstrom;
        OpenMM_System_setDefaultPeriodicBoxVectors(system, a, b, c);
    }
}

Example 20 with Crystal

use of ffx.crystal.Crystal in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addFixedChargeNonBondedForce.

/**
 * Uses arithmetic mean to define sigma and geometric mean for epsilon.
 */
private void addFixedChargeNonBondedForce() {
    VanDerWaals vdW = super.getVdwNode();
    if (vdW == null) {
        return;
    }
    /**
     * Only 6-12 LJ with arithmetic mean to define sigma and geometric mean
     * for epsilon is supported.
     */
    VanDerWaalsForm vdwForm = vdW.getVDWForm();
    if (vdwForm.vdwType != LENNARD_JONES || vdwForm.radiusRule != ARITHMETIC || vdwForm.epsilonRule != GEOMETRIC) {
        logger.info(format(" VDW Type:         %s", vdwForm.vdwType));
        logger.info(format(" VDW Radius Rule:  %s", vdwForm.radiusRule));
        logger.info(format(" VDW Epsilon Rule: %s", vdwForm.epsilonRule));
        logger.log(Level.SEVERE, String.format(" Unsuppporterd van der Waals functional form."));
        return;
    }
    fixedChargeNonBondedForce = OpenMM_NonbondedForce_create();
    /**
     * OpenMM vdW force requires a diameter (i.e. not radius).
     */
    double radScale = 1.0;
    if (vdwForm.radiusSize == RADIUS) {
        radScale = 2.0;
    }
    /**
     * OpenMM vdw force requires atomic sigma values (i.e. not r-min).
     */
    if (vdwForm.radiusType == R_MIN) {
        radScale /= 1.122462048309372981;
    }
    /**
     * Add particles.
     */
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        VDWType vdwType = atom.getVDWType();
        double sigma = OpenMM_NmPerAngstrom * vdwType.radius * radScale;
        double eps = OpenMM_KJPerKcal * vdwType.wellDepth;
        double charge = 0.0;
        MultipoleType multipoleType = atom.getMultipoleType();
        if (multipoleType != null && atoms[i].getElectrostatics()) {
            charge = multipoleType.charge;
        }
        OpenMM_NonbondedForce_addParticle(fixedChargeNonBondedForce, charge, sigma, eps);
    }
    /**
     * Define 1-4 scale factors.
     */
    double lj14Scale = vdwForm.getScale14();
    double coulomb14Scale = 1.0 / 1.2;
    ParticleMeshEwald pme = super.getPmeNode();
    Bond[] bonds = super.getBonds();
    if (bonds != null && bonds.length > 0) {
        int nBonds = bonds.length;
        PointerByReference bondArray;
        bondArray = OpenMM_BondArray_create(0);
        for (int i = 0; i < nBonds; i++) {
            Bond bond = bonds[i];
            int i1 = bond.getAtom(0).getXyzIndex() - 1;
            int i2 = bond.getAtom(1).getXyzIndex() - 1;
            OpenMM_BondArray_append(bondArray, i1, i2);
        }
        if (pme != null) {
            coulomb14Scale = pme.getScale14();
        }
        OpenMM_NonbondedForce_createExceptionsFromBonds(fixedChargeNonBondedForce, bondArray, coulomb14Scale, lj14Scale);
        OpenMM_BondArray_destroy(bondArray);
        int num = OpenMM_NonbondedForce_getNumExceptions(fixedChargeNonBondedForce);
        chargeExclusion = new boolean[num];
        vdWExclusion = new boolean[num];
        exceptionChargeProd = new double[num];
        exceptionEps = new double[num];
        IntByReference particle1 = new IntByReference();
        IntByReference particle2 = new IntByReference();
        DoubleByReference chargeProd = new DoubleByReference();
        DoubleByReference sigma = new DoubleByReference();
        DoubleByReference eps = new DoubleByReference();
        for (int i = 0; i < num; i++) {
            OpenMM_NonbondedForce_getExceptionParameters(fixedChargeNonBondedForce, i, particle1, particle2, chargeProd, sigma, eps);
            if (abs(chargeProd.getValue()) > 0.0) {
                chargeExclusion[i] = false;
                exceptionChargeProd[i] = chargeProd.getValue();
            } else {
                exceptionChargeProd[i] = 0.0;
                chargeExclusion[i] = true;
            }
            if (abs(eps.getValue()) > 0.0) {
                vdWExclusion[i] = false;
                exceptionEps[i] = eps.getValue();
            } else {
                vdWExclusion[i] = true;
                exceptionEps[i] = 0.0;
            }
        }
    }
    Crystal crystal = super.getCrystal();
    if (crystal.aperiodic()) {
        OpenMM_NonbondedForce_setNonbondedMethod(fixedChargeNonBondedForce, OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_NoCutoff);
    } else {
        OpenMM_NonbondedForce_setNonbondedMethod(fixedChargeNonBondedForce, OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_PME);
        if (pme != null) {
            // Units of the Ewald coefficient are A^-1; Multiply by AngstromsPerNM to convert to (Nm^-1).
            double aEwald = OpenMM_AngstromsPerNm * pme.getEwaldCoefficient();
            int nx = pme.getReciprocalSpace().getXDim();
            int ny = pme.getReciprocalSpace().getYDim();
            int nz = pme.getReciprocalSpace().getZDim();
            OpenMM_NonbondedForce_setPMEParameters(fixedChargeNonBondedForce, aEwald, nx, ny, nz);
        }
        NonbondedCutoff nonbondedCutoff = vdW.getNonbondedCutoff();
        double off = nonbondedCutoff.off;
        double cut = nonbondedCutoff.cut;
        OpenMM_NonbondedForce_setCutoffDistance(fixedChargeNonBondedForce, OpenMM_NmPerAngstrom * off);
        OpenMM_NonbondedForce_setUseSwitchingFunction(fixedChargeNonBondedForce, OpenMM_True);
        if (cut == off) {
            logger.warning(" OpenMM does not properly handle cutoffs where cut == off!");
            if (cut == Double.MAX_VALUE || cut == Double.POSITIVE_INFINITY) {
                logger.info(" Detected infinite or max-value cutoff; setting cut to 1E+40 for OpenMM.");
                cut = 1E40;
            } else {
                logger.info(String.format(" Detected cut %8.4g == off %8.4g; scaling cut to 0.99 of off for OpenMM.", cut, off));
                cut *= 0.99;
            }
        }
        OpenMM_NonbondedForce_setSwitchingDistance(fixedChargeNonBondedForce, OpenMM_NmPerAngstrom * cut);
    }
    OpenMM_NonbondedForce_setUseDispersionCorrection(fixedChargeNonBondedForce, OpenMM_False);
    // OpenMM_Force_setForceGroup(fixedChargeNonBondedForce, 1);
    OpenMM_System_addForce(system, fixedChargeNonBondedForce);
    logger.log(Level.INFO, String.format(" Added fixed charge non-bonded force."));
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        addCustomGBForce();
    }
}