NAMD
FreeEnergyMain.C File Reference
`#include <string.h>`
`#include <iostream.h>`
`#include <strstream.h>`
`#include "FreeEnergyEnums.h"`
`#include "FreeEnergyAssert.h"`
`#include "FreeEnergyGroup.h"`
`#include "Vector.h"`
`#include "FreeEnergyVector.h"`
`#include "FreeEnergyRestrain.h"`
`#include "FreeEnergyRMgr.h"`
`#include "FreeEnergyLambda.h"`
`#include "FreeEnergyLambdMgr.h"`
`#include "GlobalMasterFreeEnergy.h"`

Go to the source code of this file.

void main ()

## Function Documentation

 void main ( )

Definition at line 27 of file FreeEnergyMain.C.

27  {
28
30
31  char AStr[] =
32  "urestraint { \
33  posi (sn, 1) kf=20 ref=(, 0,0,0) \
34  dist (sn, 1) (sn, 2) kf= 10, ref = 10 \
35  angl (sn, 1) (sn, 2) (sn, 3) kf=5, ref=180 \
36  dihe (sn,1)(sn 2)(sn,3)(sn 4),barr=10 ref=90 \
37  posi bound group { (sn1, 1) to (sn1, 3) }, kf=10, low = (1,2, 3 4) \
38  dist bound (sn1, 1, cb) (sn1, 2, cb) kf=5, hi=10 \
39  angle bound group { (sn, 1) (sn, 3) } (sn, 5), (sn, 6), kf = 3,low=90 \
40  dihe bound (sn, 1) (sn,2) (sn 3),(sn ,4) gap=5, low=5, hi = 10, delta= 2 \
41  posi pmf (sn, 1, ca) kf=10, low=(1,2,3), high = ( 4 5 6) \
42  dist pmf (sn, 1, ca) (sn, 2, ca) kf = 10 low = 3 hi=2 \
43  angle pmf (sn 1 ca) (sn 2 ca) group {(sn 3 ca) (sn 4 ca)} kf=1 low=90 hi=180 \
44  dihe pmf (sn 1) (sn 2) (sn,3,ca) (sn,4,ca) barr= 5, low = 45 hi=135 \
45  } \
46  urestraint { \
47  dist pmf group { (insulin, 10) to (insulin, 15) } \
48  group { (insulin, 30) to (insulin, 35) } kf=20, low=20, hi=10 \
49  } \
50  pmf { \
52  time = 30 fs \
53  print = 8.fs\
54  } \
55  mcti { \
57  time = 30fs \
58  print = 4fs \
59  } \
60  urestraint { \
61  dist (insulin, 10, ca) (insulin, 20, cb) kf = 10 ref=3; \
62  } \
63  urestraint { \
64  angle (insulin,10) (insulin,20) (insulin,30) kf=10 ref=3; \
65  dist pmf (sn, 1, ca) (sn, 2, ca) kf = 10 low = 3 hi=2 \
66  } \
67  pmf { \
69  } \
70  pmf { \
72  } \
73  mcti{\
75  equiltime=12 fs \
76  accumtime = 12fs \
77  numsteps \
78  3 \
79  } \
80  pmf { \
82  time = 200 fs \
83  print = 25 fs \
84  } \
85  pmf { \
87  time = 205 fs \
88  print = 27 fs \
89  } \
90  pmf { \
92  lambda = 0.88 \
93  } \
94  pmf { \
96  lambda = 0.55 \
97  } \
98  pmf { \
100  lambdat=.44 \
101  } \
102  pmf { \
104  lambda=.33 \
105  } \
106  pmf { \
108  time = 3ps \
109  lambda = 1.0 \
110  lambdat = 0.5 \
111  print = 40.fs \
112  accumtime = 100. fs \
113  equiltime = 4 \
114  } \
115  ";
116
117  // put everything into the istrstream
118  istrstream* pInput;
119  pInput = new istrstream(AStr);
120  CFE.SetConfig(pInput);
121  CFE.user_initialize();
122
123  // this is what's executed every time-step