3.7 Gradients/Forces

The solvent forces acting on the atoms in a molecule may be calculated using the CalcForces method. The components of the forces are set to a float array of length 3N, where N is the number of atoms. The components of the gradient are equal in magnitude to the force, but have the opposite sign.

 1 /*******************************************************************************
 2  * Copyright (C) 2006, 2008 OpenEye Scientific Software, Inc.
 3  ******************************************************************************/
 4 package openeye.examples.oezap;
 5
 6 import openeye.oechem.*;
 7 import openeye.oezap.*;
 8
 9 public class ZapForces {
10   public static void main(String argv[]) {
11     if (argv.length != 1) {
12       System.err.println("usage: ZapForces <molfile>");
13       System.exit(1);
14     }
15
16     OEZap zap = new OEZap();
17     zap.SetInnerDielectric(1.0f);
18     zap.SetGridSpacing(0.5f);
19
20     oemolistream ifs = new oemolistream();
21     if (!ifs.open(argv[0])) {
22       System.err.println("Unable to open file for reading: " + argv[0]);
23       System.exit(1);
24     }
25     OEGraphMol mol = new OEGraphMol();
26     while (oechem.OEReadMolecule(ifs, mol)) {
27       System.out.println("\nForce Components for " + mol.GetTitle()
28           + ", in kT/Angstrom");
29       System.out.println("Index\tElement\t-dE/dx\t\t-dE/dy\t\t-dE/dz");
30       OEFloatArray forces = new OEFloatArray(mol.GetMaxAtomIdx() * 3);
31       oechem.OEAssignBondiVdWRadii(mol);
32       oechem.OEMMFFAtomTypes(mol);
33       oechem.OEMMFF94PartialCharges(mol);
34       zap.SetMolecule(mol);
35       zap.CalcForces(forces.ptrCast());
36       OEAtomBaseIter aiter = mol.GetAtoms();
37       while (aiter.hasNext()) {
38         OEAtomBase atom = aiter.next();
39         System.out.println(atom.GetIdx() + "\t"
40             + oechem.OEGetAtomicSymbol(atom.GetAtomicNum()) + "\t"
41             + forces.getItem(atom.GetIdx()) + "\t"
42             + forces.getItem(atom.GetIdx() + 1) + "\t"
43             + forces.getItem(atom.GetIdx() + 2));
44       }
45     }
46     ifs.close();
47   }
48 }

Listing:3.9 Calculating Solvation Forces

				ZAP Electrostatics at OpenEye Java Programming Manual

				ZAP Electrostatics at OpenEye Java Programming Manual