AMBER Archive (2004)

Subject: Re: AMBER: simulated annealing

From: Abd Ghani Bin Abd Aziz (GS13161_at_mutiara.upm.edu.my)
Date: Wed Jul 28 2004 - 08:22:37 CDT

Dear Amber,

Thank you for your reply. i already create a new script with nmropt=1. i
also removed the group definition (as your advice-actually i want to
restraint but at mean time i just want to see wether the temperature can
cool down or not). the script that i creat, i put it at the bottom of the
email. as u mention about the output file, it seems that everything is
fine. i paste also the output file for you to look at it. thank you.

Abd Ghani

 # Control section
 &cntrl
  ntwx = 250, ntpr = 50,
  ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
  ntb = 2, ntc = 2, ntf = 2,
  nstlim = 21000, dt = 0.0010,
  ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
  ibelly = 0, ntr = 0,
  imin = 0, irest = 0, ntx = 1, nmropt = 1,
 &end

 &ewald
  skinnb = 2.0,
  nbflag = 1,
 &end

 &wt
  type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
 &end

 &wt
  type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
  400.0,
 &end

 &wt
  type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
  10.0,
 &end

 &wt
  type='END'
 &end
 &rst
  iat = 0,
 &end
END

________________________________________________________________________

Here is the input file:

 # Control section
 &cntrl
  ntwx = 250, ntpr = 50,
  ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,
  ntb = 2, ntc = 2, ntf = 2,
  nstlim = 21000, dt = 0.0010,
  ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
  ibelly = 0, ntr = 0,
  imin = 0, irest = 0, ntx = 1, nmropt = 1,
 &end

 &ewald
  skinnb = 2.0,
  nbflag = 1,
 &end

 &wt
  type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,
 &end

 &wt
  type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =
  400.0,
 &end

 &wt
  type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =
  10.0,
 &end

 &wt
  type='END'
 &end
 &rst
  iat = 0,
 &end
END
-------------------------------------------------------------------------

   1. RESOURCE USE:

 getting box info from bottom of parm
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found

   EWALD SPECIFIC INPUT:

     Largest sphere to fit in unit cell has radius = 32.575
     Calculating ew_coeff from dsum_tol,cutoff
     Box X = 79.791 Box Y = 79.791 Box Z = 79.791
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

 NATOM = 33896 NTYPES = 17 NBONH = 31021 MBONA = 2952
 NTHETH = 6594 MTHETA = 4023 NPHIH = 11772 MPHIA = 7184
 NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 9744
 NBONA = 2952 NTHETA = 4023 NPHIA = 7184 NUMBND = 44
 NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1
 IFBOX = 2 NMXRS = 24 IFCAP = 0

   EWALD MEMORY USE:

| Total heap storage needed = 1245
| Adjacent nonbond minimum mask = 69551
| Max number of pointers = 25
| List build maxmask = 139102
| Maximage = 49591

   EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 1245
| Size of EEDTABLE = 20918
| Real memory needed by EEDTABLE = 83672
| Integer memory needed by ADJ = 139102
| Integer memory used by local nonb= 1232919
| Real memory used by local nonb = 555525

| MAX NONBOND PAIRS = 100000000

| Memory Use Allocated Used
| Real 10000000 1963082
| Hollerith 10000000 213122
| Integer 10000000 2119605

| Max Nonbonded Pairs:********

     BOX TYPE: TRUNCATED OCTAHEDRON

   2. CONTROL DATA FOR THE RUN

     TIMLIM= 999999. IREST = 0 IBELLY= 0
     IMIN = 0
     IPOL = 0

     NTX = 1 NTXO = 1
     IG = 71277 TEMPI = 10.00 HEAT = 0.000

     NTB = 2 BOXX = 79.791
     BOXY = 79.791 BOXZ = 79.791

     NTT = 1 TEMP0 = 400.000
     DTEMP = 0.000 TAUTP = 1.000
     VLIMIT= 0.000

     NTP = 1 PRES0 = 1.000 COMP = 44.600
     TAUP = 0.100 NPSCAL= 0

     NTCM = 0 NSCM = 9999999

     NSTLIM=21000 NTU = 1
     T = 0.000 DT = 0.00100

     NTC = 2 TOL = 0.00001 JFASTW = 0

     NTF = 2 NSNB = 25

     CUT = 8.000 SCNB = 2.000
     SCEE = 1.200 DIELC = 1.000

     NTPR = 50 NTWR = 50 NTWX = 250
     NTWV = 0 NTWE = 0 IOUTFM= 0
     NTWPRT= 0 NTWPR0= 0 NTAVE= 0

     NTR = 0 NTRX = 1
     TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000

     IVCAP = 0 MATCAP= 0 FCAP = 1.500

   OTHER DATA:

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

     VRAND= 0

     NATOM = 33896 NRES = 9744

     Water definition for fast triangulated model:
     Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2

   3. ATOMIC COORDINATES AND VELOCITIES

 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 1 2000 10.000000 400.000000 0 0
 TEMP0 2001 3000 400.000000 400.000000 0 0
 TEMP0 3001 21000 400.000000 10.000000 0 0

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

 Number of triangulated 3-point waters found: 9377

     Sum of charges from parm topology file = -0.00000023
     Forcing neutrality...
 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
 ---------------------------------------------------
     Total number of mask terms = 59876
     Total number of mask terms = 119752
| Total Ewald setup time = 0.09999990
  ------------------------------------------------------------------------------

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