AMBER Archive (2009)

Subject: [AMBER] problem in pressure equillibration

From: wong105_at_llnl.gov
Date: Tue Jun 16 2009 - 01:18:22 CDT

Hi;

    I'm using amber 8 to equilibrate a 43286 atom system. After
heating the system to 300
K, 25ps (1fs timesteps, ntt=3) of NVT simulation followed (also at
300K). When I start
the pressure equillibration, I get the following error:

ASSERTion 'xtindex <= 10 .and. xtindex >= 0' failed in ew_direct.f at
line 943.

The input file I used is:

  &cntrl
    imin = 0,
    irest=1,
    ntx=5,
    ntpr = 100,
    ntwx = 100,
    ntwe = 100,
    iwrap=1,
    ntwr = 1000,
    nstlim =10000,
    dt = 0.001,
    ntb = 2,
    cut = 11,
    ntr = 0,
    ntc = 2,
    ntf = 2,
    nmropt = 0,
    ntt = 1,
    temp0 = 300.0,
    ntp=1,
    pres0=1.0,
    taup=10,
  &end

Note I tried using taup=3 and 5 before setting this parameter to 10.
Has anyone observed
this behavior before? Some ofthe output is below:

| Flags: MPI
  getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 39.009
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/09 Time = 01:52:16
  NATOM = 43286 NTYPES = 17 NBONH = 41720 MBONA = 1593
  NTHETH = 3642 MTHETA = 2148 NPHIH = 6709 MPHIA = 3819
  NHPARM = 0 NPARM = 0 NNB = 70976 NRES = 13575
  NBONA = 1593 NTHETA = 2148 NPHIA = 3819 NUMBND = 62
  NUMANG = 125 NPTRA = 48 NATYP = 45 NPHB = 1
  IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
  NCOPY = 0

| Memory Use Allocated
| Real 3049515
| Hollerith 273293
| Integer 2260012
| Max Pairs 330206
| Max Rstack 1227492
| Max Istack 216430
| Total 45445 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

......
   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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8168E-11 at 2.732560
  ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 192434
| TOTAL SIZE OF NONBOND LIST = 18371501

  NSTEP = 100 TIME(PS) = 85.100 TEMP(K) = 300.94 PRESS
= -255.0
  Etot = -106228.7798 EKtot = 26353.5248 EPtot =
-132582.3046
  BOND = 551.9689 ANGLE = 1656.7456 DIHED =
1400.9006
  1-4 NB = 716.6664 1-4 EEL = 9639.4064 VDWAALS =
17214.2505
  EELEC = -163762.2430 EHBOND = 0.0000 RESTRAINT =
    0.0000
  EKCMT = 11944.6498 VIRIAL = 14825.1260 VOLUME =
523250.0270
                                                     Density =
    0.8354
  Ewald error estimate: 0.6977E-05
   
------------------------------------------------------------------------------

  NSTEP = 200 TIME(PS) = 85.200 TEMP(K) = 300.69 PRESS
= -323.9
  Etot = -106235.4052 EKtot = 26331.7631 EPtot =
-132567.1683
  BOND = 577.8501 ANGLE = 1681.5169 DIHED =
1398.3593
  1-4 NB = 698.7472 1-4 EEL = 9611.1972 VDWAALS =
17231.8852
  EELEC = -163766.7241 EHBOND = 0.0000 RESTRAINT =
    0.0000
  EKCMT = 12004.2147 VIRIAL = 15662.5754 VOLUME =
523186.6971
                                                     Density =
    0.8355
  Ewald error estimate: 0.6196E-05
   
------------------------------------------------------------------------------

  NSTEP = 300 TIME(PS) = 85.300 TEMP(K) = 300.05 PRESS
= -359.8
  Etot = -106244.9948 EKtot = 26275.5856 EPtot =
-132520.5804
  BOND = 552.7989 ANGLE = 1668.2645 DIHED =
1420.1295
  1-4 NB = 711.0346 1-4 EEL = 9663.4828 VDWAALS =
16953.2163
  EELEC = -163489.5071 EHBOND = 0.0000 RESTRAINT =
    0.0000
  EKCMT = 12032.4122 VIRIAL = 16096.5153 VOLUME =
523113.0068

  Ewald error estimate: 0.3080E-04
   
------------------------------------------------------------------------------

  NSTEP = 400 TIME(PS) = 85.400 TEMP(K) = 299.88 PRESS
= -347.5
  Etot = -106253.9265 EKtot = 26260.5138 EPtot =
-132514.4404
  BOND = 594.7058 ANGLE = 1622.2264 DIHED =
1404.7160
  1-4 NB = 706.1265 1-4 EEL = 9685.9846 VDWAALS =
16848.4413
  EELEC = -163376.6410 EHBOND = 0.0000 RESTRAINT =
    0.0000
  EKCMT = 11923.5027 VIRIAL = 15847.3449 VOLUME =
523030.9328
                                                     Density =
    0.8358
  Ewald error estimate: 0.5722E-04
   
------------------------------------------------------------------------------

(the output ends at this point).

Any ideas will be greatly appreciated.

Thanks;

-Sergio

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