AMBER Archive (2008)

Subject: AMBER: Minimizaton stops after Ncyc steps only

From: mon_sharma_at_research.iiit.ac.in
Date: Mon Sep 15 2008 - 11:34:22 CDT

Dear All,
I am new AMBER10 user. As far as I could understand the manual, and
tutorial, I prepared one RNA system for doing MD simulations with TIP3P
water. When I am trying to minimize the system, the minimization stops
after steepest descent only, and not going further for conjugate gradient.
The calculation stops abruptly. Moreover when I use SHAKE, it gives LINMIN
failure, but when I dont use SHAKE, it gives EEL and EAMBER as ********.
The input file I took as:

input for minimization with restraints
  &cntrl
   imin = 1,
   ntmin = 1,
   dx0 = 0.02,
   maxcyc = 15000,
   ncyc = 7000,
   ntpr = 100,
   ntwr = 100,
   ntwx = 100,
   ntwv = 100,
   ntwe = 100,
   cut = 12,
   iwrap = 1,
   ntt = 3,
   ntr = 1,
   ntb = 1,
   ntc = 1,
  /
  &ewald
   ew_type = 0, verbose =0,
   order = 4
  /
Hold the RNA fixed
500.0
RES 1 162
END
END

And the output file is:
--------------------------------------------------------------------------------
    1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
  getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 37.922
| New format PARM file being parsed.
| Version = 1.000 Date = 09/11/08 Time = 21:19:04
  NATOM = 64295 NTYPES = 19 NBONH = 60646 MBONA = 3905
  NTHETH = 4033 MTHETA = 6093 NPHIH = 8994 MPHIA = 11075
  NHPARM = 0 NPARM = 0 NNB = 108007 NRES = 19951
  NBONA = 3905 NTHETA = 6093 NPHIA = 11075 NUMBND = 45
  NUMANG = 88 NPTRA = 41 NATYP = 31 NPHB = 1
  IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
  NCOPY = 0
| Memory Use Allocated
| Real 4199389
| Hollerith 405723
| Integer 1806687
| Max Pairs 58808493
| nblistReal 771540
| nblist Int 2197918
| Total 285783 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

      BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
    2. CONTROL DATA FOR THE RUN
-------------------------------------------------------------------------------
eneral flags:
      imin = 1, nmropt = 0

Nature and format of input:
      ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
      ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
100
      iwrap = 1, ntwx = 100, ntwv = 100, ntwe =
100
      ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0

Potential function:
      ntf = 1, ntb = 1, igb = 0, nsnb =
25
      ipol = 0, gbsa = 0, iesp = 0
      dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
      scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
      ibelly = 0, ntr = 1

Energy minimization:
      maxcyc = 15000, ncyc = 7000, ntmin = 1
      dx0 = 0.02000, drms = 0.00010

Ewald parameters:
      verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
      vdwmeth = 1, eedmeth = 1, netfrc = 0
      Box X = 103.434 Box Y = 75.845 Box Z = 104.570
      Alpha = 90.000 Beta = 90.000 Gamma = 90.000
      NFFT1 = 108 NFFT2 = 75 NFFT3 = 108
      Cutoff= 12.000 Tol =0.100E-04
      Ewald Coefficient = 0.22664
      Interpolation order = 4

     LOADING THE CONSTRAINED ATOMS AS GROUPS

    5. REFERENCE ATOM COORDINATES

     ----- READING GROUP 1; TITLE:
  Hold the RNA fixed
     GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
  GRP 1 RES 1 TO 162
       Number of atoms in this group = 5250
     ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
    3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

  begin time read from input coords = 0.000 ps

  Number of triangulated 3-point waters found: 19628

      Sum of charges from parm topology file = -0.00000014
      Forcing neutrality...
   4. RESULTS
--------------------------------------------------------------------------------

  ---------------------------------------------------
  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 = 0.3146E-14 at 2.553520
| CHECK d/dx switch(x): max rel err = 0.7933E-11 at 2.712040
  ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 29724073
| TOTAL SIZE OF NONBOND LIST = 29724073

    NSTEP ENERGY RMS GMAX NAME NUMBER
       1 -2.5691E+04 4.7469E+03 1.0290E+06 O 47646

  BOND = 185.0610 ANGLE = 6320.6711 DIHED =
3600.1754
  VDWAALS = 144433.7532 EEL = -165420.7272 HBOND =
0.0000
  1-4 VDW = 3364.2477 1-4 EEL = -18174.1796 RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
     100 -3.5619E+06 2.3706E+08 6.4100E+10 H2 31370

  BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
  VDWAALS = 20229.8168 EEL = -3607696.2833 HBOND =
0.0000
  1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
  EAMBER = -3580011.2945

    NSTEP ENERGY RMS GMAX NAME NUMBER
     200 -3.3009E+07 2.9205E+10 7.8970E+12 O 31419

  BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
  VDWAALS = 20229.8162 EEL = ************* HBOND =
0.0000
  1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
  EAMBER = *************

------------------------------
-------------------------------- and so on the calc to 7000.

    NSTEP ENERGY RMS GMAX NAME NUMBER
    6900 -3.1597E+07 2.6711E+10 7.2226E+12 O 31419

  BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
  VDWAALS = 20229.8162 EEL = ************* HBOND =
0.0000
  1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
  EAMBER = *************

    NSTEP ENERGY RMS GMAX NAME NUMBER
    7000 -1.1928E+07 3.5494E+09 9.5976E+11 H2 31370

  BOND = 14633.5684 ANGLE = 5112.5799 DIHED =
3723.1738
  VDWAALS = 20229.8164 EEL = ************* HBOND =
0.0000
  1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT =
18115.3132
  EAMBER = *************

and here the calculation stops. I am missing something. But
can't figure out what. If anyone can please help me out..
Thanking you,
Regards,
Monika

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