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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Received on Wed Nov 10 2004 - 00:53:00 PST
