0NOTE


source of yout184

server:/B/bpti/bpti4d30/bpti.9/cold.0_32.564free


summaries of description/input/output of simulation

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


FILE _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, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAU
 &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 = 32768,                                                                
 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 = 128,                                                                    
 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                                                                           
         7         0         0         0         0         0         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, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAU

 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=32768       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  =     128    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


            7   0.00000
            0         0         0         0         0         0         0
          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
      0.00000   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 =    77.046 ps

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


          ENTERING INTO DYNAMICS

 NB-UPDATE: NPAIRS =   82653  HBPAIR =    4935

    571    2   19    1  347  348  349  350  571    7    0
       0.08934     0.00000     0.00000     3.14159  -800.00000     0.00000
       0.08934     0.99601     0.08922     0.08922    -5.30000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       5.30000     3.14159     3.19072  -800.00000  -800.00000  -800.00000
tor=  571 phi=   0.089 psi=   3.142 epw=     3.191 df=  -800.000 dum=   0.000
T   571       1   0.089   3.142     3.191  -800.000   -71.379   0.000

    572    3   19    1  347  354  353  350  572    7    0
       0.09773     0.00000     0.00000     3.14159  -800.00000     0.00000
       0.09773     0.99523     0.09758     0.09758    -5.30000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       5.30000     3.14159     3.81764  -800.00000  -800.00000  -800.00000
tor=  572 phi=   0.098 psi=   3.142 epw=     3.818 df=  -800.000 dum=   0.000
T   572       1   0.098   3.142     3.818  -800.000   -78.062   0.000

    573    1    9    1  347  346  345  355  573    7    0
       1.03806     0.00000     0.00000     4.17308  -410.83300  -686.45192
       1.03806     0.50789     0.86142     0.86142     1.00000     0.00000
       0.00100     0.00000     1.03149     0.00000     1.00000   800.00000
       1.00000     0.00000     0.01728    -6.10398    -6.10398  -410.83300
tor=  573 phi=   1.038 psi=   4.173 epw=     0.017 df=    -6.104 dum=   0.000
T   573       1   1.038   4.173     0.017    -6.104    -5.258   0.000

    575    4   17    1  348  347  354  353  575    7    0
       6.23914     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.23914     0.99903    -0.04403    -0.04403    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.77590  -800.00000  -800.00000  -800.00000
tor=  575 phi=   6.239 psi=   3.142 epw=     0.776 df=  -800.000 dum=   0.000
T   575       1   6.239   3.142     0.776  -800.000    35.226   0.000

    576    5    3    1  348  349  350  353  576    7    0
       6.24461     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.24461     0.99926    -0.03857    -0.03857    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.59524  -800.00000  -800.00000  -800.00000
tor=  576 phi=   6.245 psi=   3.142 epw=     0.595 df=  -800.000 dum=   0.000
T   576       1   6.245   3.142     0.595  -800.000    30.855   0.000

    577    6   17    1  349  348  347  354  577    7    0
       6.23561     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.23561     0.99887    -0.04756    -0.04756    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     0.90537  -800.00000  -800.00000  -800.00000
tor=  577 phi=   6.236 psi=   3.142 epw=     0.905 df=  -800.000 dum=   0.000
T   577       1   6.236   3.142     0.905  -800.000    38.050   0.000

    578    7    3    1  349  350  353  354  578    7    0
       6.22564     0.00000     0.00000     3.14159  -800.00000     0.00000
       6.22564     0.99834    -0.05752    -0.05752    -2.65000     0.00000
       0.00100     0.00000     0.00000     0.00000     1.00000   800.00000
       2.65000     3.14159     1.32430  -800.00000  -800.00000  -800.00000
tor=  578 phi=   6.226 psi=   3.142 epw=     1.324 df=  -800.000 dum=   0.000
T   578       1   6.226   3.142     1.324  -800.000    46.012   0.000
DQ       1    -0.051    -0.051     0.323   158.722   163.844     0.010   0.001

 NSTEP =     1  TIME(PS) =   77.047  TEMP(K) =    97.23  PRESS =      0.00
 Etot   =   -1775.3199  EKtot   =     159.2990  EPtot      =   -1934.6189
 BOND   =      64.8590  ANGLE   =      98.0946  DIHED      =     158.5864
 1-4 NB =     109.9679  1-4 EEL =    1918.4761  NONBOND    =    -430.4641
 NBEEL  =   -3822.7758  EHBOND  =     -31.3630  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------

 NB-UPDATE: NPAIRS =   83521  HBPAIR =    4965
 NB-UPDATE: NPAIRS =   83332  HBPAIR =    4977
 NB-UPDATE: NPAIRS =   83224  HBPAIR =    4966
 NB-UPDATE: NPAIRS =   83026  HBPAIR =    4942
 NB-UPDATE: NPAIRS =   83267  HBPAIR =    4942
tor=  571 phi=   0.025 psi=   3.142 epw=     0.251 df=  -800.000 dum=   0.000
tor=  572 phi=   6.252 psi=   3.142 epw=     0.400 df=  -800.000 dum=   0.000
T   573     128   1.028   4.173     0.063     2.988     2.488   0.000
tor=  573 phi=   1.023 psi=   4.173 epw=     0.031 df=     8.198 dum=   0.000
tor=  575 phi=   0.037 psi=   3.142 epw=     0.547 df=  -800.000 dum=   0.000
tor=  576 phi=   6.260 psi=   3.142 epw=     0.220 df=  -800.000 dum=   0.000
tor=  577 phi=   6.251 psi=   3.142 epw=     0.424 df=  -800.000 dum=   0.000
tor=  578 phi=   0.026 psi=   3.142 epw=     0.270 df=  -800.000 dum=   0.000
DQ     128    -1.531    -1.480     0.432   157.059   163.844     0.010   0.001

 NSTEP =   128  TIME(PS) =   77.174  TEMP(K) =    96.84  PRESS =      0.00
 Etot   =   -1774.1954  EKtot   =     158.6610  EPtot      =   -1932.8564
 BOND   =      68.2180  ANGLE   =     109.4946  DIHED      =     146.6162
 1-4 NB =     110.7943  1-4 EEL =    1916.9039  NONBOND    =    -431.7135
 NBEEL  =   -3818.7316  EHBOND  =     -34.4383  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


[deleted many lines]

 ------------------------------------------------------------------------------
 NSTEP = 32640  TIME(PS) =  109.686  TEMP(K) =    94.95  PRESS =      0.00
 Etot   =   -1772.7474  EKtot   =     155.5716  EPtot      =   -1928.3190
 BOND   =      60.7279  ANGLE   =     106.4963  DIHED      =     159.7351
 1-4 NB =     108.8149  1-4 EEL =    1920.0933  NONBOND    =    -431.2624
 NBEEL  =   -3819.9567  EHBOND  =     -32.9673  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------

 NB-UPDATE: NPAIRS =   82875  HBPAIR =    4946
 NB-UPDATE: NPAIRS =   83574  HBPAIR =    4969
 NB-UPDATE: NPAIRS =   83761  HBPAIR =    4993
 NB-UPDATE: NPAIRS =   83832  HBPAIR =    4995
 NB-UPDATE: NPAIRS =   83180  HBPAIR =    4960

      RESULT OF LEAST SQUARE FIT OVER 3276 STEPS
      ENERGY DRIFT PER STEP =     -0.000947     ETOT(AT X=0) = -1.772E+03

   KE Trans =     0.0000   KE Rot =     0.0000   C.O.M. Vel =    0.000000
tor=  571 phi=   6.248 psi=   3.142 epw=     0.492 df=  -800.000 dum=   0.000
tor=  572 phi=   6.273 psi=   3.142 epw=     0.043 df=  -800.000 dum=   0.000
T   573   32768   1.027   4.173     0.147     4.133     3.368   0.000
tor=  573 phi=   1.071 psi=   4.173 epw=     0.624 df=   -36.005 dum=   0.000
tor=  575 phi=   0.030 psi=   3.142 epw=     0.359 df=  -800.000 dum=   0.000
tor=  576 phi=   0.054 psi=   3.142 epw=     1.163 df=  -800.000 dum=   0.000
tor=  577 phi=   6.275 psi=   3.142 epw=     0.028 df=  -800.000 dum=   0.000
tor=  578 phi=   6.252 psi=   3.142 epw=     0.389 df=  -800.000 dum=   0.000
DQ   32768    11.323     0.480    -0.319   169.237   163.844     0.010   0.001

 NSTEP = 32768  TIME(PS) =  109.814  TEMP(K) =   102.76  PRESS =      0.00
 Etot   =   -1773.8059  EKtot   =     168.3589  EPtot      =   -1942.1648
 BOND   =      56.0046  ANGLE   =     105.6727  DIHED      =     148.1808
 1-4 NB =     112.5951  1-4 EEL =    1929.0287  NONBOND    =    -430.1704
 NBEEL  =   -3830.7533  EHBOND  =     -32.7230  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


      RESULT OF LEAST SQUARE FIT OVER    8 STEPS
      ENERGY DRIFT PER STEP =     -0.106761     ETOT(AT X=0) = -1.773E+03

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

     %MD-I-AVERAGES1, for the last  32768 steps


 NSTEP = 32768  TIME(PS) =  109.814  TEMP(K) =   100.02  PRESS =      0.00
 Etot   =   -1773.6630  EKtot   =     163.8786  EPtot      =   -1937.5417
 BOND   =      56.7051  ANGLE   =     105.9885  DIHED      =     149.5984
 1-4 NB =     110.3315  1-4 EEL =    1919.8348  NONBOND    =    -430.8898
 NBEEL  =   -3817.1177  EHBOND  =     -31.9926  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


 %MD-I-AVERAGES2, RMS fluctuations


 NSTEP = 32768  TIME(PS) =  109.814  TEMP(K) =     2.92  PRESS =      0.00
 Etot   =       1.5728  EKtot   =       4.7777  EPtot      =       5.2054
 BOND   =       3.9232  ANGLE   =       4.2526  DIHED      =       5.0325
 1-4 NB =       2.6955  1-4 EEL =       4.8059  NONBOND    =       3.7662
 NBEEL  =       7.7467  EHBOND  =       1.1131  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------


     Routine      Sec       %
     --------------------------
     Pairlist    556.55    1.35
     Nonbond   32698.63   79.11
     Bond        189.94    0.46
     Angle       865.74    2.09
     Dihedral   4789.64   11.59
     Shake       256.70    0.62
     Pol. der      0.00    0.00
     Efielde       0.00    0.00
     Indip         0.00    0.00
     Matmul        0.00    0.00
     Other      1976.48    4.78
     --------------------------
     Total     41333.68   11.48 Hours



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

FILE _mdttyout.long

 
  Amber 4.0 united atom _ dynamics simulation
md cont. run: at , 100K, .001x32768ps, 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_32.564free -f -c ../cold.0/cold.0_10x/_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=128 		nstlim=32768
 
removing old output files..

MINMD: 
 
No errors detected

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


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

FILE mdin

md cont. run: at , 100K, .001x32768ps, 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 = 32768, 
 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 = 128, 
 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
         7         0         0         0         0         0         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


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

FILE mdinfo


 NSTEP = 32768  TIME(PS) =  109.814  TEMP(K) =   102.76  PRESS =      0.00
 Etot   =   -1773.8059  EKtot   =     168.3589  EPtot      =   -1942.1648
 BOND   =      56.0046  ANGLE   =     105.6727  DIHED      =     148.1808
 1-4 NB =     112.5951  1-4 EEL =    1929.0287  NONBOND    =    -430.1704
 NBEEL  =   -3830.7533  EHBOND  =     -32.7230  CONSTRAINT =       0.0000



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


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
