AMBER Archive (2004)

Subject: AMBER: single strand simulation

From: ding (bj_0206_at_yahoo.com)
Date: Tue Nov 09 2004 - 18:12:17 CST

Dear Amber Users,
 
I'm using Amber7 to do a MD simulation of a single strand DNA with a modified base in explicit water. The protocol is same as DNA tutorial on Amber website, except using ntt=1 for temperature control. But the simulation got error termination with vlimit and shake problem. Any suggestion is appreciated.
 
Here is the MD input file,
"
50ps production, 9 cut, at 285k
 &cntrl

  ntx = 7, irest = 1,
  ntpr = 200, ntwx = 500,

  ntf = 2, ntb = 2,
  cut = 9.0,

  ibelly = 0, ntr = 0,

  imin = 0,

  nstlim = 25000,
  t = 0.0, dt = 0.002,

  temp0 = 285.0, tempi = 285.0,
  ntt = 1,
  tautp = 4.0,

  ntp = 1, pres0 = 1.0,
  taup = 4.0,

  ntc = 2,

 &end
"

 

 

 

And the output file,

"
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: SGIFFT MPI HAS_FTN_ERFC
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 11/01/04 Time = 19:40:10
 NATOM = 11752 NTYPES = 18 NBONH = 11505 MBONA = 266
 NTHETH = 332 MTHETA = 413 NPHIH = 647 MPHIA = 741
 NHPARM = 0 NPARM = 0 NNB = 17314 NRES = 3809
 NBONA = 266 NTHETA = 413 NPHIA = 741 NUMBND = 46
 NUMANG = 101 NPTRA = 46 NATYP = 28 NPHB = 1
 IFBOX = 1 NMXRS = 68 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 2000000 876639
| Hollerith 400000 74323
| Integer 2000000 670870

| Max Nonbonded Pairs: 5400000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 7, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 200, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

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

Molecular dynamics:
     nstlim = 25000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 285.00000, tempi = 285.00000, heat = 0.00000
     dtemp = 5.00000, tautp = 4.00000

Pressure regulation:
     ntp = 1, plevel = 1
     pres0 = 1.00000, comp = 44.60000, taup = 4.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
     Box X = 50.985 Box Y = 47.921 Box Z = 65.030
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 50 NFFT2 = 48 NFFT3 = 72
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR

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

 NEW EWALD BOX PARAMETERS from inpcrd file:
     A = 50.98501 B = 47.92147 C = 65.02955

     ALPHA = 90.00000 BETA = 90.00000 GAMMA = 90.00000

                                                                                
 begin time read from input coords = 50.000 ps

 Number of triangulated 3-point waters found: 3788
| Atom division among processors:
| 0 5878 11752
| Running AMBER/MPI version on 2 nodes

     Sum of charges from parm topology file = 0.00000008
     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 = 0.2088E-14 at 2.598900
| CHECK d/dx switch(x): max rel err = 0.7671E-11 at 2.757160
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1297697
| TOTAL SIZE OF NONBOND LIST = 2858452

 NSTEP = 200 TIME(PS) = 50.400 TEMP(K) = 282.99 PRESS = -595.4
 Etot = -32488.3672 EKtot = 6677.4766 EPtot = -39165.8438
 BOND = 94.5234 ANGLE = 223.9095 DIHED = 251.9361
 1-4 NB = 104.6471 1-4 EEL = -1273.2334 VDWAALS = 5238.4105
 EELEC = -43806.0370 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 3142.6618 VIRIAL = 5180.5581 VOLUME = 158535.9494
                                                Density = 0.7541
 Ewald error estimate: 0.4143E-04
 ------------------------------------------------------------------------------

 NSTEP = 400 TIME(PS) = 50.800 TEMP(K) = 283.75 PRESS = -273.3
 Etot = -32490.9763 EKtot = 6695.2508 EPtot = -39186.2270
 BOND = 92.8575 ANGLE = 201.3605 DIHED = 249.5058
 1-4 NB = 109.6833 1-4 EEL = -1274.0289 VDWAALS = 5428.9774
 EELEC = -43994.5827 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 3227.8900 VIRIAL = 4161.5366 VOLUME = 158247.2903
                                                Density = 0.7555
 Ewald error estimate: 0.1029E-03
 ------------------------------------------------------------------------------

 NSTEP = 600 TIME(PS) = 51.200 TEMP(K) = 283.69 PRESS = -595.6
 Etot = -32494.7825 EKtot = 6693.8169 EPtot = -39188.5994
 BOND = 93.7550 ANGLE = 207.9467 DIHED = 246.2635
 1-4 NB = 114.0400 1-4 EEL = -1269.2966 VDWAALS = 5195.5147
 EELEC = -43776.8228 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 3233.8357 VIRIAL = 5264.8120 VOLUME = 157921.2314
                                                Density = 0.7571
 Ewald error estimate: 0.6558E-04
 ------------------------------------------------------------------------------

 vlimit exceeded for step 684; vmax = 20.11661747007105

 NSTEP = 800 TIME(PS) = 51.600 TEMP(K) = 291.38 PRESS = -485.8
 Etot = -32200.9562 EKtot = 6875.3971 EPtot = -39076.3533
 BOND = 100.0771 ANGLE = 268.7120 DIHED = 271.0628
 1-4 NB = 122.7877 1-4 EEL = -1232.6946 VDWAALS = 5329.0342
 EELEC = -43935.3325 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 3254.4675 VIRIAL = 4907.1574 VOLUME = 157568.1818
                                                Density = 0.7588
 Ewald error estimate: 0.1403E-04
 ------------------------------------------------------------------------------

check COM velocity, temp: 0.000002 0.00(Removed)

 NSTEP = 1000 TIME(PS) = 52.000 TEMP(K) = 293.96 PRESS = -638.2
 Etot = -32227.0443 EKtot = 6936.2671 EPtot = -39163.3114
 BOND = 131.8887 ANGLE = 264.3709 DIHED = 251.4868
 1-4 NB = 112.6335 1-4 EEL = -1285.2691 VDWAALS = 5284.8711
 EELEC = -43923.2933 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 3274.0849 VIRIAL = 5440.9814 VOLUME = 157247.2932
                                                Density = 0.7603
 Ewald error estimate: 0.1879E-03
 ------------------------------------------------------------------------------

 vlimit exceeded for step 1032; vmax = 36.59493060837673
 vlimit exceeded for step 1040; vmax = 55.36025888544626

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 74 240 241

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

                        
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