src/types/OplsTorsionType.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file OplsTorsionType.hpp
 * @author    teng lin
 * @date  11/16/2004
 * @version 1.0
 */ 

#ifndef TYPES_OPLSTORSIONTYPE_HPP
#define TYPES_OPLSTORSIONTYPE_HPP

#include "types/PolynomialTorsionType.hpp"

namespace oopse {

  /**
   * @class OplsTorsionType OplsTorsionType.hpp "types/OplsTorsionType.hpp"
   * These torsion types are defined identically with functional form given
   * in the following paper:
   *
   * "Development and Testing of the OPLS All-Atom Force Field on 
   * Conformational Energetics and Properties of Organic Liquids,"  by
   * William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives, 
   * J. Am. Chem. Soc.; 1996; 118(45) pp 11225 - 11236;
   * DOI: 10.1021/ja9621760
   *
   * This torsion potential has the form:
   * 
   *  Vtors = 0.5* (v1*(1+cos(phi)) + v2*(1-cos(2*phi)) + v3*(1+cos(3*phi)))
   *
   * Notes: 
   * 
   * 1) OOPSE converts internally to a Polynomial torsion type because
   *    all of the phase angles are zero in the OPLS paper.
   * 2) Coefficients are assumed to be in kcal / mol, and be careful about
   *    that factor of 1/2 when importing the coefficients!
   */
  class OplsTorsionType : public PolynomialTorsionType{
    
  public:
    
    OplsTorsionType(RealType v1, RealType v2, RealType v3) :  
      PolynomialTorsionType(), v1_(v1), v2_(v2), v3_(v3) {
      
      //convert OPLS Torsion Type to Polynomial Torsion type
      RealType c0 = v2 + 0.5 * (v1 + v3);
      RealType c1 = 0.5 * (v1 - 3.0 * v3);
      RealType c2 = -v2;
      RealType c3 = 2.0 * v3;
      c0 = c0/2;
      c1 = c1/2;
      c2 = c2/2;
      c3 = c3/2;
      // I change the parameter to half to see if this is the problem.
      setCoefficient(0, c0);
      setCoefficient(1, c1);
      setCoefficient(2, c2);
      setCoefficient(3, c3);
    }
    
    friend std::ostream& operator <<(std::ostream& os, OplsTorsionType& ott);
    
  private:
    
    RealType v1_;
    RealType v2_;
    RealType v3_;
    
  };
  
  std::ostream& operator <<(std::ostream& os, OplsTorsionType& ott) {
    
    os << "This OplsTorsionType has below form:" << std::endl;
    os << ott.v1_ << "/2*(1+cos(phi))" << " + "
       << ott.v2_ << "/2*(1-cos(2*phi))" << " + "
       << ott.v3_ << "/2*(1+cos(3*phi))" << std::endl;
    return os;
  }
  
  
} //end namespace oopse
#endif //TYPES_OPLSTORSIONTYPE_HPP


Revision:	3446
Committed:	Wed Sep 10 19:51:45 2008 UTC (15 years, 9 months ago) by cli2
File size:	4433 byte(s)
Log Message:	Inversion fixes and amber mostly working
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file OplsTorsionType.hpp
44	* @author teng lin
45	* @date 11/16/2004
46	* @version 1.0
47	*/
48
49	#ifndef TYPES_OPLSTORSIONTYPE_HPP
50	#define TYPES_OPLSTORSIONTYPE_HPP
51
52	#include "types/PolynomialTorsionType.hpp"
53
54	namespace oopse {
55
56	/**
57	* @class OplsTorsionType OplsTorsionType.hpp "types/OplsTorsionType.hpp"
58	* These torsion types are defined identically with functional form given
59	* in the following paper:
60	*
61	* "Development and Testing of the OPLS All-Atom Force Field on
62	* Conformational Energetics and Properties of Organic Liquids," by
63	* William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives,
64	* J. Am. Chem. Soc.; 1996; 118(45) pp 11225 - 11236;
65	* DOI: 10.1021/ja9621760
66	*
67	* This torsion potential has the form:
68	*
69	* Vtors = 0.5* (v1(1+cos(phi)) + v2(1-cos(2phi)) + v3(1+cos(3*phi)))
70	*
71	* Notes:
72	*
73	* 1) OOPSE converts internally to a Polynomial torsion type because
74	* all of the phase angles are zero in the OPLS paper.
75	* 2) Coefficients are assumed to be in kcal / mol, and be careful about
76	* that factor of 1/2 when importing the coefficients!
77	*/
78	class OplsTorsionType : public PolynomialTorsionType{
79
80	public:
81
82	OplsTorsionType(RealType v1, RealType v2, RealType v3) :
83	PolynomialTorsionType(), v1_(v1), v2_(v2), v3_(v3) {
84
85	//convert OPLS Torsion Type to Polynomial Torsion type
86	RealType c0 = v2 + 0.5 * (v1 + v3);
87	RealType c1 = 0.5 * (v1 - 3.0 * v3);
88	RealType c2 = -v2;
89	RealType c3 = 2.0 * v3;
90	c0 = c0/2;
91	c1 = c1/2;
92	c2 = c2/2;
93	c3 = c3/2;
94	// I change the parameter to half to see if this is the problem.
95	setCoefficient(0, c0);
96	setCoefficient(1, c1);
97	setCoefficient(2, c2);
98	setCoefficient(3, c3);
99	}
100
101	friend std::ostream& operator <<(std::ostream& os, OplsTorsionType& ott);
102
103	private:
104
105	RealType v1_;
106	RealType v2_;
107	RealType v3_;
108
109	};
110
111	std::ostream& operator <<(std::ostream& os, OplsTorsionType& ott) {
112
113	os << "This OplsTorsionType has below form:" << std::endl;
114	os << ott.v1_ << "/2*(1+cos(phi))" << " + "
115	<< ott.v2_ << "/2(1-cos(2phi))" << " + "
116	<< ott.v3_ << "/2(1+cos(3phi))" << std::endl;
117	return os;
118	}
119
120
121	} //end namespace oopse
122	#endif //TYPES_OPLSTORSIONTYPE_HPP
123
124