| Bsoft 2.0.5 Bernard's software package

rwmd.h
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1
9 #include "rwatomprop.h"
10 #include "Vector3.h"
11
12 #ifndef _Bmd_
13 #define _Bmd_
14 /************************************************************************
15 @Object: struct Bbondtype
16 @Description:
17 A structure for a bond type.
18 @Features:
19 This defines all the properties of a bond type.
20 *************************************************************************/
21 struct Bbondtype {
22 Bbondtype* next;
23 char type1[8]; // Atom type 1
24 char type2[8]; // Atom type 2
25 float covlength; // Covalent bond length
26 float vdwdist; // Van der Waals interaction distance
27 long number; // Number of this type
28 float std; // Standard deviation of covalent bond length
29 } ;
30
31 /************************************************************************
32 @Object: struct Bangletype
33 @Description:
34 A structure for an angle type.
35 @Features:
36 This defines all the properties of an angle type.
37 *************************************************************************/
38 struct Bangletype {
39 Bangletype* next;
40 char type1[8]; // Atom type 1
41 char type2[8]; // Atom type 2
42 char type3[8]; // Atom type 3
43 float angle; // Angle
44 long number; // Number of this type
45 float std; // Standard deviation of angle
46 } ;
47
48 /************************************************************************
49 @Object: struct Bmd
50 @Description:
51 A structure used for molecular mechanics.
52 @Features:
53 This defines variables and constants for doing molecular dynamics or
54 other molecular mechanics.
55 *************************************************************************/
56 struct Bmd {
57 double timestep; // Integration time step for MD
58 double Kfriction; // Friction coefficient
59 double Kbond; // Bond energy constant
60 double Kangle; // Angle energy constant
61 double Kelec; // Electrostatic energy constant
62 double Kvdw; // Van der Waals energy constant
63 double Ksep; // Separation distance energy constant
64 double Kpoint; // Point force energy constant
65 double Kmap; // Density map energy constant
66 double VdWcoeff1; // First Van der Waals coefficient (default 1/12)
67 double VdWcoeff2; // Second Van der Waals coefficient (default 1/6)
68 double sepdist; // Separation distance grid sampling
69 double cutoff; // Distance cutoff for non-bonded calculations
70 double pointdecay; // Decay constant for the point force
71 int bondsteps; // Number of sampling intervals along a bond
72 int wrap; // Flag to turn periodic boundaries on
73 double Ebond; // Bond energy
74 double Eangle; // Angle energy
75 double Eelec; // Electrostatic energy
76 double Evdw; // Van der Waals energy
77 double Esep; // Separation distance energy (overlap penalty)
78 double Epoint; // Point force energy
79 double Emap; // Density map associated energy
80 double Ekin; // Kinetic energy
81 double Epot; // Potential energy
82 Vector3<float> point; // Center of point force
83 Batomtype* atom; // Linked list of atom types
84 Bbondtype* bond; // Linked list of bond types
85 Bangletype* angle; // Linked list of angle types
86 } ;
87 #endif
88
89 // Function prototypes
90 Bmd* md_init();
91 Bmd* md_init_with_types();
92 Bmd* read_md_parameters(Bstring& filename);
93 int write_md_parameters(Bstring& filename, Bmd* md);
94 int md_kill(Bmd* md);
95
Bangletype::type1
char type1[8]
Definition: rwmd.h:40
Bmd::point
Vector3< float > point
Definition: rwmd.h:82
Bmd::Epoint
double Epoint
Definition: rwmd.h:78
Bangletype::angle
float angle
Definition: rwmd.h:43
Bbondtype::vdwdist
float vdwdist
Definition: rwmd.h:26
Bmd::Ksep
double Ksep
Definition: rwmd.h:63
Bbondtype::number
long number
Definition: rwmd.h:27
Bmd::Emap
double Emap
Definition: rwmd.h:79
Bmd
Definition: rwmd.h:56
Bbondtype::covlength
float covlength
Definition: rwmd.h:25
Bmd::Kmap
double Kmap
Definition: rwmd.h:65
write_md_parameters
int write_md_parameters(Bstring &filename, Bmd *md)
Writing molecular dynamics parameters to a STAR file.
Definition: rwmd.cpp:237
md_init_with_types
Bmd * md_init_with_types()
Initializes a molecular dynamics structure.
Definition: rwmd.cpp:51
Bangletype::next
Bangletype * next
Definition: rwmd.h:39
Bmd::Ebond
double Ebond
Definition: rwmd.h:73
Bmd::angle
Bangletype * angle
Definition: rwmd.h:85
Bmd::Evdw
double Evdw
Definition: rwmd.h:76
Bbondtype::type2
char type2[8]
Definition: rwmd.h:24
Bangletype::std
float std
Definition: rwmd.h:45
Bmd::Kpoint
double Kpoint
Definition: rwmd.h:64
Bmd::Esep
double Esep
Definition: rwmd.h:77
Bmd::pointdecay
double pointdecay
Definition: rwmd.h:70
Bmd::Kbond
double Kbond
Definition: rwmd.h:59
Bmd::Kfriction
double Kfriction
Definition: rwmd.h:58
Batomtype
Definition: rwatomprop.h:19
rwatomprop.h
Header file for reading atom property files.
Bmd::Kelec
double Kelec
Definition: rwmd.h:61
Bbondtype::next
Bbondtype * next
Definition: rwmd.h:22
Bmd::Eelec
double Eelec
Definition: rwmd.h:75
Bangletype::number
long number
Definition: rwmd.h:44
Bbondtype::type1
char type1[8]
Definition: rwmd.h:23
read_md_parameters
Bmd * read_md_parameters(Bstring &filename)
Reading molecular dynamics parameters from STAR files.
Definition: rwmd.cpp:80
Bmd::Kangle
double Kangle
Definition: rwmd.h:60
Bangletype::type2
char type2[8]
Definition: rwmd.h:41
Bstring
Definition: Bstring.h:29
Bangletype
Definition: rwmd.h:38
Bmd::Epot
double Epot
Definition: rwmd.h:81
Bmd::wrap
int wrap
Definition: rwmd.h:72
Vector3< float >
Bmd::VdWcoeff2
double VdWcoeff2
Definition: rwmd.h:67
Bmd::sepdist
double sepdist
Definition: rwmd.h:68
Vector3.h
Class for 3-value vectors.
Bmd::cutoff
double cutoff
Definition: rwmd.h:69
Bmd::atom
Batomtype * atom
Definition: rwmd.h:83
Bmd::timestep
double timestep
Definition: rwmd.h:57
Bmd::Eangle
double Eangle
Definition: rwmd.h:74
Bangletype::type3
char type3[8]
Definition: rwmd.h:42
Bbondtype::std
float std
Definition: rwmd.h:28
Bmd::VdWcoeff1
double VdWcoeff1
Definition: rwmd.h:66
md_init
Bmd * md_init()
Initializes a molecular dynamics structure.
Definition: rwmd.cpp:28
Bbondtype
Definition: rwmd.h:21
Bmd::bond
Bbondtype * bond
Definition: rwmd.h:84
md_kill
int md_kill(Bmd *md)
Deallocates a molecular dynamics structure.
Definition: rwmd.cpp:417
Bmd::Ekin
double Ekin
Definition: rwmd.h:80
Bmd::bondsteps
int bondsteps
Definition: rwmd.h:71
Bmd::Kvdw
double Kvdw
Definition: rwmd.h:62