#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.
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Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved. Definition at line 27 of file FreeEnergyMain.C. References GlobalMasterFreeEnergy::user_calculate(), and GlobalMasterFreeEnergy::user_initialize(). 00027 {
00028
00029 GlobalMasterFreeEnergy CFE;
00030
00031 char AStr[] =
00032 "urestraint { \
00033 posi (sn, 1) kf=20 ref=(, 0,0,0) \
00034 dist (sn, 1) (sn, 2) kf= 10, ref = 10 \
00035 angl (sn, 1) (sn, 2) (sn, 3) kf=5, ref=180 \
00036 dihe (sn,1)(sn 2)(sn,3)(sn 4),barr=10 ref=90 \
00037 posi bound group { (sn1, 1) to (sn1, 3) }, kf=10, low = (1,2, 3 4) \
00038 dist bound (sn1, 1, cb) (sn1, 2, cb) kf=5, hi=10 \
00039 angle bound group { (sn, 1) (sn, 3) } (sn, 5), (sn, 6), kf = 3,low=90 \
00040 dihe bound (sn, 1) (sn,2) (sn 3),(sn ,4) gap=5, low=5, hi = 10, delta= 2 \
00041 posi pmf (sn, 1, ca) kf=10, low=(1,2,3), high = ( 4 5 6) \
00042 dist pmf (sn, 1, ca) (sn, 2, ca) kf = 10 low = 3 hi=2 \
00043 angle pmf (sn 1 ca) (sn 2 ca) group {(sn 3 ca) (sn 4 ca)} kf=1 low=90 hi=180 \
00044 dihe pmf (sn 1) (sn 2) (sn,3,ca) (sn,4,ca) barr= 5, low = 45 hi=135 \
00045 } \
00046 urestraint { \
00047 dist pmf group { (insulin, 10) to (insulin, 15) } \
00048 group { (insulin, 30) to (insulin, 35) } kf=20, low=20, hi=10 \
00049 } \
00050 pmf { \
00051 task = grow, \
00052 time = 30 fs \
00053 print = 8.fs\
00054 } \
00055 mcti { \
00056 task = up, \
00057 time = 30fs \
00058 print = 4fs \
00059 } \
00060 urestraint { \
00061 dist (insulin, 10, ca) (insulin, 20, cb) kf = 10 ref=3; \
00062 } \
00063 urestraint { \
00064 angle (insulin,10) (insulin,20) (insulin,30) kf=10 ref=3; \
00065 dist pmf (sn, 1, ca) (sn, 2, ca) kf = 10 low = 3 hi=2 \
00066 } \
00067 pmf { \
00068 task = down \
00069 } \
00070 pmf { \
00071 task = fade \
00072 } \
00073 mcti{\
00074 task=stepup; \
00075 equiltime=12 fs \
00076 accumtime = 12fs \
00077 numsteps \
00078 3 \
00079 } \
00080 pmf { \
00081 task = stop \
00082 time = 200 fs \
00083 print = 25 fs \
00084 } \
00085 pmf { \
00086 task = nogrow \
00087 time = 205 fs \
00088 print = 27 fs \
00089 } \
00090 pmf { \
00091 task = stop \
00092 lambda = 0.88 \
00093 } \
00094 pmf { \
00095 task = nogrow \
00096 lambda = 0.55 \
00097 } \
00098 pmf { \
00099 task = nogrow \
00100 lambdat=.44 \
00101 } \
00102 pmf { \
00103 task = stop \
00104 lambda=.33 \
00105 } \
00106 pmf { \
00107 task = up \
00108 time = 3ps \
00109 lambda = 1.0 \
00110 lambdat = 0.5 \
00111 print = 40.fs \
00112 accumtime = 100. fs \
00113 equiltime = 4 \
00114 } \
00115 ";
00116
00117 // put everything into the istrstream
00118 istrstream* pInput;
00119 pInput = new istrstream(AStr);
00120 CFE.SetConfig(pInput);
00121 CFE.user_initialize();
00122
00123 // this is what's executed every time-step
00124 int SomeNum = 10000;
00125 for (int i=0; i<SomeNum; i++) {
00126 CFE.user_calculate();
00127 }
00128
00129 }
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1.3.9.1