Examples with TitrationESV ffx.potential.extended.TitrationESV used on opensource projects

Example 1 with TitrationESV

use of ffx.potential.extended.TitrationESV in project ffx by mjschnie.

the class PhMD method readyup.

private void readyup() {
    // Create MultiTerminus objects to wrap termini.
    if (config.titrateTermini) {
        for (Residue res : mola.getResidueList()) {
            if (res.getPreviousResidue() == null || res.getNextResidue() == null) {
                MultiTerminus multiTerminus = new MultiTerminus(res, ff, ffe, mola);
                Polymer polymer = findResiduePolymer(res, mola);
                polymer.addMultiTerminus(res, multiTerminus);
                reInitialize(true, false);
                titratingTermini.add(multiTerminus);
                logger.info(String.format(" Titrating: %s", multiTerminus));
            }
        }
    }
    /* Create containers for titratables: MultiResidues for discrete, ExtendedVariables for continuous. */
    if (distribution == Distribution.CONTINUOUS) {
        esvSystem = new ExtendedSystem(mola);
        esvSystem.setConstantPh(pH);
        for (Residue res : chosenResidues) {
            MultiResidue multi = TitrationUtils.titratingMultiresidueFactory(mola, res);
            TitrationESV esv = new TitrationESV(esvSystem, multi);
            titratingESVs.add(esv);
            for (Residue background : multi.getInactive()) {
                inactivateResidue(background);
            }
            esvSystem.addVariable(esv);
        }
        ffe.attachExtendedSystem(esvSystem);
        logger.info(format(" Continuous pHMD readied with %d residues.", titratingESVs.size()));
    } else {
        for (Residue res : chosenResidues) {
            // Create MultiResidue objects to wrap titratables.
            MultiResidue multiRes = new MultiResidue(res, ff, ffe);
            Polymer polymer = findResiduePolymer(res, mola);
            polymer.addMultiResidue(multiRes);
            recursiveMap(res, multiRes);
            // Switch back to the original form and ready the ForceFieldEnergy.
            multiRes.setActiveResidue(res);
            reInitialize(true, false);
            titratingMultis.add(multiRes);
            logger.info(String.format(" Titrating: %s", multiRes));
        }
        logger.info(format(" Discrete MCMD readied with %d residues.", titratingMultis.size()));
    }
    switch(distribution) {
        default:
        case DISCRETE:
            molDyn.setMonteCarloListener(this, MonteCarloNotification.EACH_STEP);
            break;
        case CONTINUOUS:
            ffe.attachExtendedSystem(esvSystem);
            molDyn.attachExtendedSystem(esvSystem, 100);
            break;
    }
}