1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
6 //
7 // This file is part of Force Field X.
8 //
9 // Force Field X is free software; you can redistribute it and/or modify it
10 // under the terms of the GNU General Public License version 3 as published by
11 // the Free Software Foundation.
12 //
13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16 // details.
17 //
18 // You should have received a copy of the GNU General Public License along with
19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20 // Place, Suite 330, Boston, MA 02111-1307 USA
21 //
22 // Linking this library statically or dynamically with other modules is making a
23 // combined work based on this library. Thus, the terms and conditions of the
24 // GNU General Public License cover the whole combination.
25 //
26 // As a special exception, the copyright holders of this library give you
27 // permission to link this library with independent modules to produce an
28 // executable, regardless of the license terms of these independent modules, and
29 // to copy and distribute the resulting executable under terms of your choice,
30 // provided that you also meet, for each linked independent module, the terms
31 // and conditions of the license of that module. An independent module is a
32 // module which is not derived from or based on this library. If you modify this
33 // library, you may extend this exception to your version of the library, but
34 // you are not obligated to do so. If you do not wish to do so, delete this
35 // exception statement from your version.
36 //
37 // ******************************************************************************
38 package ffx.potential.openmm;
39
40 import ffx.openmm.Force;
41 import ffx.openmm.HarmonicBondForce;
42 import ffx.potential.bonded.UreyBradley;
43 import ffx.potential.parameters.UreyBradleyType;
44
45 import java.util.logging.Level;
46 import java.util.logging.Logger;
47
48 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_KJPerKcal;
49 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_NmPerAngstrom;
50 import static java.lang.String.format;
51
52 /**
53 * Urey-Bradley Force.
54 */
55 public class UreyBradleyForce extends HarmonicBondForce {
56
57 private static final Logger logger = Logger.getLogger(UreyBradleyForce.class.getName());
58
59 /**
60 * Urey-Bradly Force constructor.
61 *
62 * @param openMMEnergy The OpenMMEnergy instance that contains the Urey-Bradley terms.
63 */
64 public UreyBradleyForce(OpenMMEnergy openMMEnergy) {
65 UreyBradley[] ureyBradleys = openMMEnergy.getUreyBradleys();
66 if (ureyBradleys == null || ureyBradleys.length < 1) {
67 return;
68 }
69
70 double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
71
72 for (UreyBradley ureyBradley : ureyBradleys) {
73 int i1 = ureyBradley.getAtom(0).getXyzIndex() - 1;
74 int i2 = ureyBradley.getAtom(2).getXyzIndex() - 1;
75 UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
76 double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
77 // The implementation of UreyBradley in FFX & Tinker: k x^2
78 // The implementation of Harmonic Bond Force in OpenMM: k x^2 / 2
79 double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
80 addBond(i1, i2, length, k);
81 }
82
83 int forceGroup = openMMEnergy.getMolecularAssembly().getForceField().getInteger("UREY_BRADLEY_FORCE", 0);
84 setForceGroup(forceGroup);
85 logger.log(Level.INFO, format(" Urey-Bradleys \t%6d\t\t%1d", ureyBradleys.length, forceGroup));
86 }
87
88 /**
89 * Convenience method to construct an OpenMM Urey-Bradley Force.
90 *
91 * @param openMMEnergy The OpenMM Energy instance that contains the angles.
92 * @return An OpenMM Urey-Bradley Force, or null if there are no Urey-Bradley.
93 */
94 public static Force constructForce(OpenMMEnergy openMMEnergy) {
95 UreyBradley[] ureyBradleys = openMMEnergy.getUreyBradleys();
96 if (ureyBradleys == null || ureyBradleys.length < 1) {
97 return null;
98 }
99 return new UreyBradleyForce(openMMEnergy);
100 }
101
102 /**
103 * Update the Urey-Bradley parameters in the OpenMM Context.
104 *
105 * @param openMMEnergy The OpenMM Energy instance that contains the Urey-Bradley terms.
106 */
107 public void updateForce(OpenMMEnergy openMMEnergy) {
108 UreyBradley[] ureyBradleys = openMMEnergy.getUreyBradleys();
109 if (ureyBradleys == null || ureyBradleys.length < 1) {
110 return;
111 }
112
113 double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
114
115 int index = 0;
116 for (UreyBradley ureyBradley : ureyBradleys) {
117 int i1 = ureyBradley.getAtom(0).getXyzIndex() - 1;
118 int i2 = ureyBradley.getAtom(2).getXyzIndex() - 1;
119 UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
120 double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
121 // The implementation of UreyBradley in FFX & Tinker: k x^2
122 // The implementation of Harmonic Bond Force in OpenMM: k x^2 / 2
123 double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
124 setBondParameters(index++, i1, i2, length, k);
125 }
126
127 updateParametersInContext(openMMEnergy.getContext());
128 }
129
130 }