0NOTE


exam1.data from y4.8.x10.2[184,], in .../bpti.9/S/.Data

exam date: March 13, 1997

----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------

ADDED ON:
Sat Oct 30 11:55:46 MST 2004

scr10.s:[240,]
"y4.8.x10.2<-matrix(scan(\"test.40_800_.1_2.dihedrals\"),ncol=1024, byrow=T)"                                   
run_anal2:anal2 -t tor -l /user2/display/exe/lists/list.dihedrals.atoms -f
1024 -p 1024 -n ../testnoepw.40_800_128_512/mdcrd |tr -s " " "\012"|sed 1,2d
>testnoepw.40_800_128_512.dihedrals


INFORMATION ON RUN:
[date or run: May  8  1994]

----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------


directory of files in this file:

/B/bpti/bpti4d30/bpti.9/test.40_800_.1_2

----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------


_mdttyout.long
 
  Amber 4.0 united atom _ dynamics simulation
md cont. run: at , 100K, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUTP=0.1, CM out
4pti Tyr-35 CONS +- 0-180, Unchrgd SC & NC United Atom, 300K, Taup=.1, IDIEL=1
../Run.test.40_800_2 -f -c ../test.40_800_1_16/_mdrestrt.long -p ../equil.0/_prmtop
  trial=0  	start_time=0     	tempi=100   	temp0=100
  ntx=5 	init=4 			irest=1 	t=100
  tautp=0.1 	dt=.001 		ntpr=8 		nstlim=2048
 
removing old output files..

MINMD: 
 
No errors detected

  WHOPPEE, we're done  (or we should be :-^)

----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------

mdin

md cont. run: at , 100K, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUTP=0.1, CM out
 &cntrl
 timlim = 999999.,
 irest = 1,
 ibelly = 0,
 kform = 1,
 ichdna = 0,
 imin = 0,
 ipol = 0,
 jptres = 62,
 ntx = 5,
 ntxo = 1,
 ig = 77752,
 tempi = 100,
 heat = 0.0,
 ntb = 0,
 iftres = 1,
 nrun = 1,
 ntt = 1,
 temp0 = 100,
 dtemp = 999.00,
 tautp = 0.1,
 tauts = 0.1,
 ntp = 0,
 pres0 = 1.0,
 comp = 44.6,
 taup = 0.2,
 npscal = 0,
 ndfmin = 0,
 ntcm = 0,
 nscm = 0,
 nstlim = 2048, 
 init = 4,
 ntu = 1,
 t = 0,
 dt = .001,
 ntc = 2,
 tol = 0.0005,
 ntf = 2,
 ntid = 0,
 ntnb = 1,
 nsnb = 25,
 idiel = 1, 
 imgslt = 0,
 cut = 9.0,
 scnb = 2.0,
 scee = 2.0,
 dielc = 1,
 ntpr = 8, 
 ntwx = 2, 
 ntwv = 0, 
 ntwe = 0,
 ntwxm = 999999,
 ntwvm = 999999,
 ntwem = 999999,
 ioutfm = 0,
 ntr = 1,
 ntrx = 1,
 ivcap = 0,
 fcap = 0.0,
 maxcyc = 2000,
 ncyc = 10,
 ntmin = 1,
 dx0 = 0.01,
 dxm = 0.5,
 dele = 0.0001,
 drms = 0.0001
 &end
         8         0         0         0         0         0         0         0
  564    1  345  346  347  348     0.128      40.0      45.2     800.0         0
  573    1  347  346  345  355     0.000      00.0      59.1     800.0         0
  571    1  347  348  349  350     0.000      00.0       0.0     800.0         0
  572    1  347  354  353  350     0.000      00.0       0.0     800.0         0
  575    1  348  347  354  353     0.000      00.0       0.0     800.0         0
  576    1  348  349  350  353     0.000      00.0       0.0     800.0         0
  577    1  349  348  347  354     0.000      00.0       0.0     800.0         0
  578    1  349  350  353  354     0.000      00.0       0.0     800.0         0



----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------


_mdout.long

          ------------------------------------------------------
          Amber 4.0 MIN-MD including polarization: double precision
           (Latest update November 1991)
          ------------------------------------------------------
 File assignments:
mdin                                                                            
mdout                                                                           
inpcrd                                                                          
prmtop                                                                          
restrt                                                                          
refc                                                                            
mdvel                                                                           
mden                                                                            
mdcrd                                                                           
mdinfo                                                                          

Here is the input file:

md cont. run: at , 100K, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUT
 &cntrl                                                                         
 timlim = 999999.,                                                              
 irest = 1,                                                                     
 ibelly = 0,                                                                    
 kform = 1,                                                                     
 ichdna = 0,                                                                    
 imin = 0,                                                                      
 ipol = 0,                                                                      
 jptres = 62,                                                                   
 ntx = 5,                                                                       
 ntxo = 1,                                                                      
 ig = 77752,                                                                    
 tempi = 100,                                                                   
 heat = 0.0,                                                                    
 ntb = 0,                                                                       
 iftres = 1,                                                                    
 nrun = 1,                                                                      
 ntt = 1,                                                                       
 temp0 = 100,                                                                   
 dtemp = 999.00,                                                                
 tautp = 0.1,                                                                   
 tauts = 0.1,                                                                   
 ntp = 0,                                                                       
 pres0 = 1.0,                                                                   
 comp = 44.6,                                                                   
 taup = 0.2,                                                                    
 npscal = 0,                                                                    
 ndfmin = 0,                                                                    
 ntcm = 0,                                                                      
 nscm = 0,                                                                      
 nstlim = 2048,                                                                 
 init = 4,                                                                      
 ntu = 1,                                                                       
 t = 0,                                                                         
 dt = .001,                                                                     
 ntc = 2,                                                                       
 tol = 0.0005,                                                                  
 ntf = 2,                                                                       
 ntid = 0,                                                                      
 ntnb = 1,                                                                      
 nsnb = 25,                                                                     
 idiel = 1,                                                                     
 imgslt = 0,                                                                    
 cut = 9.0,                                                                     
 scnb = 2.0,                                                                    
 scee = 2.0,                                                                    
 dielc = 1,                                                                     
 ntpr = 8,                                                                      
 ntwx = 2,                                                                      
 ntwv = 0,                                                                      
 ntwe = 0,                                                                      
 ntwxm = 999999,                                                                
 ntwvm = 999999,                                                                
 ntwem = 999999,                                                                
 ioutfm = 0,                                                                    
 ntr = 1,                                                                       
 ntrx = 1,                                                                      
 ivcap = 0,                                                                     
 fcap = 0.0,                                                                    
 maxcyc = 2000,                                                                 
 ncyc = 10,                                                                     
 ntmin = 1,                                                                     
 dx0 = 0.01,                                                                    
 dxm = 0.5,                                                                     
 dele = 0.0001,                                                                 
 drms = 0.0001                                                                  
 &end                                                                           
         8         0         0         0         0         0         0         0
  564    1  345  346  347  348     0.128      40.0      45.2     800.0         0
  573    1  347  346  345  355     0.000      00.0      59.1     800.0         0
  571    1  347  348  349  350     0.000      00.0       0.0     800.0         0
  572    1  347  354  353  350     0.000      00.0       0.0     800.0         0
  575    1  348  347  354  353     0.000      00.0       0.0     800.0         0
  576    1  348  349  350  353     0.000      00.0       0.0     800.0         0
  577    1  349  348  347  354     0.000      00.0       0.0     800.0         0
  578    1  349  350  353  354     0.000      00.0       0.0     800.0         0


   1.  RESOURCE USE:
 NATOM  =     591 NTYPES =      16 NBONH =     124 MBONA  =     481
 NTHETH =     199 MTHETA =     663 NPHIH =     374 MPHIA  =     917
 NHPARM =       0 NPARM  =       0 NNB   =    2565 NRES   =      62
 NBONA  =     481 NTHETA =     663 NPHIA =     917 NUMBND =      41
 NUMANG =      92 NPTRA  =      53 NATYP =      19 NPHB   =      20
 IFBOX  =       0 NMXRS  =      17 IFCAP =       0

 enter locmem

     Memory Use       Allocated      Used
     Real              650000        36386
     Integer          2000000        55609 (static)

     Max Nonbonded Pairs: 3888782 packed  2 to a machine word
pointers reset: iptres =    62  iptatm =    591


   2.  CONTROL DATA FOR THE RUN

md cont. run: at , 100K, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUT

 TIMLIM=  999999.   IREST =    1       IBELLY=    0
 KFORM =    1       ICHDNA=    0
 IMIN  =    0       IPOL  =    0       JPTRES =    62


 NTX   =    5       NTXO  =    1       NTCX   =    0
 ISEED =    77752   TEMPI =   100.00   HEAT  =    0.000

 NTB   =    0       IFTRES=    1       BOXX  =    0.000
 BOXY  =    0.000   BOXZ  =    0.000   BETA  =    0.000

 NRUN  =    1       NTT   =    1       TEMP0 =  100.000
 DTEMP =  999.000   TAUTP =    0.100   TAUTS =    0.100

 NTP   =    0       PRES0 =    1.000   COMP  =   44.600
 TAUP  =    0.200   NPSCAL=      0

 NDFMIN=    0       NTCM  =    0       NSCM  = 9999999

 NSTLIM= 2048       INIT  =    4       NTU   =    1
 T     =    0.000   DT    =   0.00100

 NTC   =    2       NTCC  =    0       NCONP =    0
 TOL   =   0.00050

 NTF   =    2       NTID  =    0       NTN   =    0
 NTNB  =    1       NSNB  =   25       IDIEL =    1
 IMGSLT=    0

 RCUT  =    9.000   SCNB  =    2.000
 SCEE  =    2.000   DIELC =    1.000

 NTPR  =       8    NTWX  =       2    NTWV  =       0
 NTWE  =       0    NTWXM =  999999    NTWVM =  999999
 NTWEM =  999999    NTPP  =       0    IOUTFM=       0

 NTR   =    1       NTRX  =    1

 IVCAP =    0       NATCAP=      0       FCAP  =    1.500

 OTHER DATA:

 IFCAP =    0       MATCAP=      0       CUTCAP=    0.000
 XCAP  =    0.000   YCAP  =    0.000   ZCAP  =    0.000

 IPTRES=    0       IPTATM=    0       NSPSOL=    0
 NSPSTR=    0       IPTSOL=   62

 NATOM =     591  NRES =     62

 %MINMD-I-MINFO, maxcyc = 2000 ncyc =   10 ntmin =    1
 dx0 =   0.01000 dxm =   0.50000 dele =   0.00010 drms =   0.00010



    LOADING THE PERIODIC CONSTRAINT INFORMATION


            8   0.00000
            0         0         0         0         0         0         0
          564         1       345       346       347       348
          573         1       347       346       345       355
          571         1       347       348       349       350
          572         1       347       354       353       350
          575         1       348       347       354       353
          576         1       348       349       350       353
          577         1       349       348       347       354
          578         1       349       350       353       354
      0.12800   0.69813   0.78889 800.00000   1.00000   0.00000
      0.00000   0.00000   1.03149 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000
      0.00000   0.00000   0.00000 800.00000   1.00000   0.00000

   3.  ATOMIC COORDINATES AND VELOCITIES

4pti Tyr-35 CONS +- 0-180, Unchrgd SC & NC United Atom, 300K, Taup=.1, IDIEL=1  
 begin time read from input coords =    97.526 ps

 %MINMD-I-NRUN, beginning MD run =  1


          ENTERING INTO DYNAMICS

 NB-UPDATE: NPAIRS =   82499  HBPAIR =    4925

    564    1    8    1  345  346  347  348  564    8    0
       0.77783     0.04907     0.04909     3.96474  -543.93499  -586.62998
       0.77783     0.71244     0.70173     0.70173     0.00000     0.00000
       0.00100     0.12800     0.78889     0.69813     1.00000   800.00000
       0.00000     0.00000     0.82130    51.64501    51.64501  -543.93499
tor=  564 phi=   0.778 psi=   3.965 epw=     0.821 df=    51.645 dum=   0.049
T   564       1   0.778   3.965     0.821    51.645    36.241   0.049

    571    3   19    1  347  348  349  350  571    8    0
       0.00393     0.00000     0.00000     3.14159  -800.00000     0.00000
       0.00393     0.99999     0.00393     0.00393    -5.30000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       5.30000     3.14159     0.00616  -800.00000  -800.00000  -800.00000
tor=  571 phi=   0.004 psi=   3.142 epw=     0.006 df=  -800.000 dum=   0.000
T   571       1   0.004   3.142     0.006  -800.000    -3.140   0.000

    572    4   19    1  347  354  353  350  572    8    0
       6.26974     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.26974     0.99991    -0.01345    -0.01345    -5.30000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       5.30000     3.14159     0.07234  -800.00000  -800.00000  -800.00000
tor=  572 phi=   6.270 psi=   3.142 epw=     0.072 df=  -800.000 dum=   0.000
T   572       1   6.270   3.142     0.072  -800.000    10.758   0.000

    573    2    9    1  347  346  345  355  573    8    0
       1.01174     0.00000     0.00000     4.17308  -410.83300  -686.45192
       1.01174     0.53039     0.84775     0.84775     1.00000     0.00000
       0.00100     0.00000     1.03149     0.00000     1.00000   800.00000
       1.00000     0.00000     0.15608    18.64008    18.64008  -410.83300
tor=  573 phi=   1.012 psi=   4.173 epw=     0.156 df=    18.640 dum=   0.000
T   573       1   1.012   4.173     0.156    18.640    15.802   0.000

    575    5   17    1  348  347  354  353  575    8    0
       0.02282     0.00000     0.00000     3.14159  -800.00000     0.00000
       0.02282     0.99974     0.02282     0.02282    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.20837  -800.00000  -800.00000  -800.00000
tor=  575 phi=   0.023 psi=   3.142 epw=     0.208 df=  -800.000 dum=   0.000
T   575       1   0.023   3.142     0.208  -800.000   -18.258   0.000

    576    6    3    1  348  349  350  353  576    8    0
       0.00573     0.00000     0.00000     3.14159  -800.00000     0.00000
       0.00573     0.99998     0.00573     0.00573    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.01312  -800.00000  -800.00000  -800.00000
tor=  576 phi=   0.006 psi=   3.142 epw=     0.013 df=  -800.000 dum=   0.000
T   576       1   0.006   3.142     0.013  -800.000    -4.581   0.000

    577    7   17    1  349  348  347  354  577    8    0
       6.26474     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.26474     0.99983    -0.01844    -0.01844    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.13608  -800.00000  -800.00000  -800.00000
tor=  577 phi=   6.265 psi=   3.142 epw=     0.136 df=  -800.000 dum=   0.000
T   577       1   6.265   3.142     0.136  -800.000    14.755   0.000

    578    8    3    1  349  350  353  354  578    8    0
       6.28231     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.28231     1.00000    -0.00088    -0.00088    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.00031  -800.00000  -800.00000  -800.00000
tor=  578 phi=   6.282 psi=   3.142 epw=     0.000 df=  -800.000 dum=   0.000
T   578       1   6.282   3.142     0.000  -800.000     0.703   0.000
DQ       1     0.122     0.122    -0.695   176.086   163.844     0.010   0.001

 NSTEP =     1  TIME(PS) =   97.527  TEMP(K) =   107.26  PRESS =      0.00
 Etot   =   -1765.9611  EKtot   =     175.7339  EPtot      =   -1941.6950
 BOND   =      37.5703  ANGLE   =      99.3169  DIHED      =     144.4640
 1-4 NB =     109.5063  1-4 EEL =    1920.9705  NONBOND    =    -420.5618
 NBEEL  =   -3801.4769  EHBOND  =     -31.4843  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------

T   564       8   0.858   4.099     3.995   105.616    79.579   0.242
tor=  564 phi=   0.957 psi=   4.198 epw=     3.902 df=    96.519 dum=   0.383
tor=  571 phi=   6.273 psi=   3.142 epw=     0.044 df=  -800.000 dum=   0.000
tor=  572 phi=   6.266 psi=   3.142 epw=     0.115 df=  -800.000 dum=   0.000
tor=  573 phi=   0.947 psi=   4.173 epw=     2.839 df=    82.947 dum=   0.000
tor=  575 phi=   6.243 psi=   3.142 epw=     0.637 df=  -800.000 dum=   0.000
tor=  576 phi=   6.237 psi=   3.142 epw=     0.871 df=  -800.000 dum=   0.000
tor=  577 phi=   0.054 psi=   3.142 epw=     1.164 df=  -800.000 dum=   0.000
tor=  578 phi=   0.061 psi=   3.142 epw=     1.508 df=  -800.000 dum=   0.000
DQ       8     1.115     0.993    -0.949   181.022   163.844     0.010   0.001

 NSTEP =     8  TIME(PS) =   97.534  TEMP(K) =   110.13  PRESS =      0.00
 Etot   =   -1749.0268  EKtot   =     180.4429  EPtot      =   -1929.4697
 BOND   =      40.0024  ANGLE   =      97.4136  DIHED      =     160.4402
 1-4 NB =     108.8648  1-4 EEL =    1921.4675  NONBOND    =    -420.7202
 NBEEL  =   -3805.6430  EHBOND  =     -31.2949  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------

.......


 ------------------------------------------------------------------------------


      RESULT OF LEAST SQUARE FIT OVER  204 STEPS
      ENERGY DRIFT PER STEP =      0.489728     ETOT(AT X=0) = -1.498E+03

   KE Trans =     0.0000   KE Rot =     0.0000   C.O.M. Vel =    0.000000
T   564    2048   0.533   3.812     7.957   225.872   109.431  -0.170
tor=  564 phi=   0.707 psi=   3.930 epw=     2.689 df=   100.911 dum=   0.000
tor=  571 phi=   6.217 psi=   3.142 epw=     1.758 df=  -800.000 dum=   0.000
tor=  572 phi=   6.264 psi=   3.142 epw=     0.153 df=  -800.000 dum=   0.000
tor=  573 phi=   0.946 psi=   4.173 epw=     2.925 df=    84.269 dum=   0.000
tor=  575 phi=   6.237 psi=   3.142 epw=     0.861 df=  -800.000 dum=   0.000
tor=  576 phi=   0.029 psi=   3.142 epw=     0.346 df=  -800.000 dum=   0.000
tor=  577 phi=   0.097 psi=   3.142 epw=     3.741 df=  -800.000 dum=   0.000
tor=  578 phi=   0.023 psi=   3.142 epw=     0.218 df=  -800.000 dum=   0.000
DQ    2048  3708.625    10.518    -4.423   293.789   163.844     0.010   0.001

 NSTEP =  2048  TIME(PS) =   99.574  TEMP(K) =   178.97  PRESS =      0.00
 Etot   =   -1417.4924  EKtot   =     293.2390  EPtot      =   -1710.7313
 BOND   =      82.8048  ANGLE   =     206.9336  DIHED      =     203.4739
 1-4 NB =     120.9884  1-4 EEL =    1905.6957  NONBOND    =    -416.3123
 NBEEL  =   -3783.1244  EHBOND  =     -31.1911  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


      RESULT OF LEAST SQUARE FIT OVER    8 STEPS
      ENERGY DRIFT PER STEP =      2.678844     ETOT(AT X=0) = -1.438E+03

   KE Trans =     0.0000   KE Rot =     0.0000   C.O.M. Vel =    0.000000

     %MD-I-AVERAGES1, for the last   2048 steps


 NSTEP =  2048  TIME(PS) =   99.574  TEMP(K) =   210.54  PRESS =      0.00
 Etot   =   -1358.3441  EKtot   =     344.9576  EPtot      =   -1703.3017
 BOND   =      81.6165  ANGLE   =     199.7325  DIHED      =     212.5959
 1-4 NB =     118.0669  1-4 EEL =    1912.5976  NONBOND    =    -411.2061
 NBEEL  =   -3786.7919  EHBOND  =     -29.9132  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


 %MD-I-AVERAGES2, RMS fluctuations


 NSTEP =  2048  TIME(PS) =   99.574  TEMP(K) =    36.56  PRESS =      0.00
 Etot   =     113.3404  EKtot   =      59.9082  EPtot      =      75.1979
 BOND   =      22.1794  ANGLE   =      37.2381  DIHED      =      32.0254
 1-4 NB =       8.5302  1-4 EEL =       9.4736  NONBOND    =       8.6675
 NBEEL  =      14.9970  EHBOND  =       1.5706  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


     Routine      Sec       %
     --------------------------
     Pairlist     34.80    1.33
     Nonbond    2015.03   77.24
     Bond         12.60    0.48
     Angle        55.63    2.13
     Dihedral    301.98   11.58
     Shake        15.93    0.61
     Pol. der      0.00    0.00
     Efielde       0.00    0.00
     Indip         0.00    0.00
     Matmul        0.00    0.00
     Other       172.88    6.63
     --------------------------
     Total      2608.85    0.72 Hours


John Rupley
 rupley@u.arizona.edu -or- jar@rupley.com
 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991
 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721
