Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2019 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "Colvar.h"
23 : #include "ActionRegister.h"
24 : #include "tools/Torsion.h"
25 :
26 : #include <string>
27 : #include <cmath>
28 :
29 : using namespace std;
30 :
31 : namespace PLMD {
32 : namespace colvar {
33 :
34 : //+PLUMEDOC COLVAR TORSION
35 : /*
36 : Calculate a torsional angle.
37 :
38 : This command can be used to compute the torsion between four atoms or alternatively
39 : to calculate the angle between two vectors projected on the plane
40 : orthogonal to an axis.
41 :
42 : \par Examples
43 :
44 : This input tells plumed to print the torsional angle between atoms 1, 2, 3 and 4
45 : on file COLVAR.
46 : \plumedfile
47 : t: TORSION ATOMS=1,2,3,4
48 : # this is an alternative, equivalent, definition:
49 : # t: TORSION VECTOR1=2,1 AXIS=2,3 VECTOR2=3,4
50 : PRINT ARG=t FILE=COLVAR
51 : \endplumedfile
52 :
53 : If you are working with a protein you can specify the special named torsion angles \f$\phi\f$, \f$\psi\f$, \f$\omega\f$ and \f$\chi_1\f$
54 : by using TORSION in combination with the \ref MOLINFO command. This can be done by using the following
55 : syntax.
56 :
57 : \plumedfile
58 : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
59 : t1: TORSION ATOMS=@phi-3
60 : t2: TORSION ATOMS=@psi-4
61 : PRINT ARG=t1,t2 FILE=colvar STRIDE=10
62 : \endplumedfile
63 :
64 : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
65 : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
66 :
67 : Both of the previous examples specify that the torsion angle should be calculated based on the position of four atoms.
68 : For the first example in particular the assumption when the torsion is specified in this way is that there are chemical
69 : bonds between atoms 1 and 2, atoms 2 and 3 and atoms 3 and 4. In general, however, a torsional angle measures the angle
70 : between two planes, which have at least one vector in common. As shown below, there is thus an alternate, more general, way
71 : through which we can define a torsional angle:
72 :
73 : \plumedfile
74 : t1: TORSION VECTOR1=1,2 AXIS=3,4 VECTOR2=5,6
75 : PRINT ARG=t1 FILE=colvar STRIDE=20
76 : \endplumedfile
77 :
78 : This input instructs PLUMED to calculate the angle between the plane containing the vector connecting atoms 1 and 2 and the vector
79 : connecting atoms 3 and 4 and the plane containing this second vector and the vector connecting atoms 5 and 6. We can even use
80 : PLUMED to calculate the torsional angle between two bond vectors around the z-axis as shown below:
81 :
82 : \plumedfile
83 : a0: FIXEDATOM AT=0,0,0
84 : az: FIXEDATOM AT=0,0,1
85 : t1: TORSION VECTOR1=1,2 AXIS=a0,az VECTOR2=5,6
86 : PRINT ARG=t1 FILE=colvar STRIDE=20
87 : \endplumedfile
88 :
89 :
90 : */
91 : //+ENDPLUMEDOC
92 :
93 872 : class Torsion : public Colvar {
94 : bool pbc;
95 : bool do_cosine;
96 :
97 : public:
98 : explicit Torsion(const ActionOptions&);
99 : // active methods:
100 : virtual void calculate();
101 : static void registerKeywords(Keywords& keys);
102 : };
103 :
104 5259 : PLUMED_REGISTER_ACTION(Torsion,"TORSION")
105 :
106 439 : void Torsion::registerKeywords(Keywords& keys) {
107 439 : Colvar::registerKeywords( keys );
108 439 : keys.add("atoms-1","ATOMS","the four atoms involved in the torsional angle");
109 439 : keys.add("atoms-2","AXIS","two atoms that define an axis. You can use this to find the angle in the plane perpendicular to the axis between the vectors specified using the VECTOR1 and VECTOR2 keywords.");
110 439 : keys.add("atoms-2","VECTOR1","two atoms that define a vector. You can use this in combination with VECTOR2 and AXIS");
111 439 : keys.add("atoms-2","VECTOR2","two atoms that define a vector. You can use this in combination with VECTOR1 and AXIS");
112 439 : keys.addFlag("COSINE",false,"calculate cosine instead of dihedral");
113 439 : }
114 :
115 438 : Torsion::Torsion(const ActionOptions&ao):
116 : PLUMED_COLVAR_INIT(ao),
117 : pbc(true),
118 440 : do_cosine(false)
119 : {
120 876 : vector<AtomNumber> atoms,v1,v2,axis;
121 438 : parseAtomList("ATOMS",atoms);
122 438 : parseAtomList("VECTOR1",v1);
123 438 : parseAtomList("VECTOR2",v2);
124 438 : parseAtomList("AXIS",axis);
125 :
126 438 : parseFlag("COSINE",do_cosine);
127 :
128 438 : bool nopbc=!pbc;
129 438 : parseFlag("NOPBC",nopbc);
130 438 : pbc=!nopbc;
131 438 : checkRead();
132 :
133 438 : if(atoms.size()==4) {
134 431 : if(!(v1.empty() && v2.empty() && axis.empty()))
135 2 : error("ATOMS keyword is not compatible with VECTOR1, VECTOR2 and AXIS keywords");
136 430 : log.printf(" between atoms %d %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial());
137 430 : atoms.resize(6);
138 430 : atoms[5]=atoms[3];
139 430 : atoms[4]=atoms[2];
140 430 : atoms[3]=atoms[2];
141 430 : atoms[2]=atoms[1];
142 7 : } else if(atoms.empty()) {
143 6 : if(!(v1.size()==2 && v2.size()==2 && axis.size()==2))
144 0 : error("VECTOR1, VECTOR2 and AXIS should specify 2 atoms each");
145 : log.printf(" between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n",
146 6 : v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial());
147 6 : atoms.resize(6);
148 6 : atoms[0]=v1[1];
149 6 : atoms[1]=v1[0];
150 6 : atoms[2]=axis[0];
151 6 : atoms[3]=axis[1];
152 6 : atoms[4]=v2[0];
153 6 : atoms[5]=v2[1];
154 2 : } else error("ATOMS should specify 4 atoms");
155 :
156 436 : if(pbc) log.printf(" using periodic boundary conditions\n");
157 104 : else log.printf(" without periodic boundary conditions\n");
158 :
159 436 : if(do_cosine) log.printf(" calculating cosine instead of torsion\n");
160 :
161 436 : addValueWithDerivatives();
162 436 : if(!do_cosine) setPeriodic("-pi","pi");
163 0 : else setNotPeriodic();
164 874 : requestAtoms(atoms);
165 436 : }
166 :
167 : // calculator
168 23955 : void Torsion::calculate() {
169 :
170 23955 : Vector d0,d1,d2;
171 23955 : if(pbc) makeWhole();
172 23955 : d0=delta(getPosition(1),getPosition(0));
173 23955 : d1=delta(getPosition(3),getPosition(2));
174 23955 : d2=delta(getPosition(5),getPosition(4));
175 23955 : Vector dd0,dd1,dd2;
176 : PLMD::Torsion t;
177 23955 : double torsion=t.compute(d0,d1,d2,dd0,dd1,dd2);
178 23955 : if(do_cosine) {
179 0 : dd0 *= -sin(torsion);
180 0 : dd1 *= -sin(torsion);
181 0 : dd2 *= -sin(torsion);
182 0 : torsion = cos(torsion);
183 : }
184 23955 : setAtomsDerivatives(0,dd0);
185 23955 : setAtomsDerivatives(1,-dd0);
186 23955 : setAtomsDerivatives(2,dd1);
187 23955 : setAtomsDerivatives(3,-dd1);
188 23955 : setAtomsDerivatives(4,dd2);
189 23955 : setAtomsDerivatives(5,-dd2);
190 :
191 23955 : setValue (torsion);
192 23955 : setBoxDerivativesNoPbc();
193 23955 : }
194 :
195 : }
196 4821 : }
197 :
198 :
199 :
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