AMBER: Trouble running molecular dynamics with an increase in temp in Sander

From: Robyn Ayscue <kajsicat.yahoo.com>
Date: Wed, 16 Jun 2004 06:43:05 -0700 (PDT)

Hi! I've been trying to run a molecular dynamics
simulation (using Sander in Amber 8) on a solvated
(TIP3/Na+), modified DNA 15-mer (holding the DNA
fixed), and after about twenty minutes or so the
program dies. In the .out file I keep getting several
vlimit errors, and the temperature seems to be
increasing exponentially until it reaches some
astronomical number and blows up. I thought I entered
the temperature control tags in the .in file
correctly-- it looks to me to be in accordance with
what's in the manual-- but maybe there's something I
missed. I've included the .out and .in files, if
anyone has a moment to take a look at them. Thanks
much!

Yours,
Robyn Ayscue


                
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5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
 &cntrl

  nmropt = 1,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,

  ntf = 2, ntb = 2,
  cut = 9.0, nsnb = 5,

  ibelly = 0, ntr = 1,

  imin = 0,
  nstlim = 12500,
  nscm = 0,
  t = 0.0, dt = 0.0005,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,

  ntc = 2, tol = 0.00001,

 &end
 &wt
   type='TEMP0', istep1=0, istep2=1000,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=1000, istep2=12500,
                 value1=300.0, value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end

500.0
RES 1 30
END
END




          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 06/15/2004 at 14:07:24
  [-O]verwriting output

File Assignments:
| MDIN: ta_md.in
| MDOUT: ta15_rus_new_fsi_md.out
|INPCRD: ta15_rus_new_fsi.crd
| PARM: ta15_rus_new_fsi.top
|RESTRT: ta15_rus_new_fsi_md.rst
| REFC: ta15_rus_new_fsi.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: ta15_rus_new_fsi_md.traj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
 &cntrl
                                                                               
  nmropt = 1,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
                                                                               
  ntf = 2, ntb = 2,
  cut = 9.0, nsnb = 5,
                                                                               
  ibelly = 0, ntr = 1,
                                                                               
  imin = 0,
  nstlim = 12500,
  nscm = 0,
  t = 0.0, dt = 0.0005,
                                                                               
  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,
                                                                               
  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,
                                                                               
  ntc = 2, tol = 0.00001,
                                                                               
 &end
 &wt
   type='TEMP0', istep1=0, istep2=1000,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=1000, istep2=12500,
                 value1=300.0, value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
                                                                               
500.0
RES 1 30
END
END
                                                                               

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


Warning: heat has been retired.
  Check the Retired Namelist Variables Appendix in the manual.

| Flags: SGIFFT
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 28.577
| New format PARM file being parsed.
| Version = 1.000 Date = 06/14/04 Time = 15:28:21
 NATOM = 21253 NTYPES = 16 NBONH = 20602 MBONA = 697
 NTHETH = 868 MTHETA = 1072 NPHIH = 1603 MPHIA = 1570
 NHPARM = 0 NPARM = 0 NNB = 32526 NRES = 6802
 NBONA = 697 NTHETA = 1072 NPHIA = 1570 NUMBND = 41
 NUMANG = 73 NPTRA = 31 NATYP = 30 NPHB = 1
 IFBOX = 1 NMXRS = 65 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 1562863
| Hollerith 134322
| Integer 1515708
| Max Pairs 9429247
| Max Rstack 1226674
| Max Istack 106265
| Total 65486 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

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

                                                                                

General flags:
     imin = 0, nmropt = 1

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

Nature and format of output:
     ntxo = 1, ntpr = 100, 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 = 5
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

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

Molecular dynamics:
     nstlim = 12500, nscm = 9999999, nrespa = 1
     t = 0.00000, dt = 0.00050, vlimit = 15.00000

Berendsen (weak-coupling) temperature regulation:
     temp0 = 300.00000, tempi = 100.00000, tautp = 0.20000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 0.20000

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

NMR refinement options:
     iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
     scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 58.580 Box Y = 81.320 Box Z = 57.153
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 60 NFFT2 = 81 NFFT3 = 60
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5. REFERENCE ATOM COORDINATES

      
    ----- READING GROUP 1; TITLE:
  &rst

     GROUP 1 HAS HARMONIC CONSTRAINTS -4.00000
 GRP 1 RES 1 TO 30
      Number of atoms in this group = 991
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   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 0 1000 100.000000 300.000000 0 0
 TEMP0 1000 12500 300.000000 300.000000 0 0

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

                  Done reading weight changes/NMR restraints


 Number of triangulated 3-point waters found: 6745

     Sum of charges from parm topology file = -0.99799987
     Assuming uniform neutralizing plasma

--------------------------------------------------------------------------------
   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 = 0.2890E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8253E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 4706485
| TOTAL SIZE OF NONBOND LIST = 4706485

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 148.23 PRESS = 10957.7
 Etot = -48895.8916 EKtot = 6356.0203 EPtot = -55251.9119
 BOND = 1172.8420 ANGLE = 963.2142 DIHED = 494.5771
 1-4 NB = 323.2520 1-4 EEL = -609.7550 VDWAALS = 11440.4954
 EELEC = -69031.3641 EHBOND = 0.0000 RESTRAINT = -5.1737
 EAMBER (non-restraint) = -55246.7382
 EKCMT = 2030.6398 VIRIAL = -62384.4795 VOLUME = 272265.2310
                                                    Density = 0.8018
 Ewald error estimate: 0.8708E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 72 ; vmax = 16.256384890227551
 vlimit exceeded for step 73 ; vmax = 16.572128161796602
 vlimit exceeded for step 74 ; vmax = 15.888771807103689
 vlimit exceeded for step 75 ; vmax = 15.223664844357604
 vlimit exceeded for step 78 ; vmax = 15.078484702829192
 vlimit exceeded for step 79 ; vmax = 15.434275004121119
 vlimit exceeded for step 80 ; vmax = 15.265850521528655
 vlimit exceeded for step 81 ; vmax = 15.027754517465915
 vlimit exceeded for step 89 ; vmax = 15.005053940573896

 NSTEP = 100 TIME(PS) = 0.050 TEMP(K) = 318.42 PRESS = -2671.6
 Etot = -53619.9992 EKtot = 13654.1591 EPtot = -67274.1584
 BOND = 1298.4252 ANGLE = 1890.2834 DIHED = 702.7767
 1-4 NB = 406.1410 1-4 EEL = -530.7234 VDWAALS = 8155.9954
 EELEC = -77004.7488 EHBOND = 0.0000 RESTRAINT = -2192.3081
 EAMBER (non-restraint) = -65081.8503
 EKCMT = 4277.1676 VIRIAL = 19473.7996 VOLUME = 263454.1942
                                                    Density = 0.8286
 Ewald error estimate: 0.2722E-04
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 185 ; vmax = 15.309668342574474
 vlimit exceeded for step 186 ; vmax = 15.218908114653411
 vlimit exceeded for step 187 ; vmax = 15.052018745926198
 vlimit exceeded for step 194 ; vmax = 15.005036626493801
 vlimit exceeded for step 195 ; vmax = 15.92360710512984
 vlimit exceeded for step 196 ; vmax = 16.100568778061159
 vlimit exceeded for step 197 ; vmax = 15.726075631985625
 vlimit exceeded for step 198 ; vmax = 15.530368792271585
 vlimit exceeded for step 199 ; vmax = 15.363151783365142

 NSTEP = 200 TIME(PS) = 0.100 TEMP(K) = 493.96 PRESS = 64.5
 Etot = -56667.8419 EKtot = 21181.3164 EPtot = -77849.1583
 BOND = 1580.1512 ANGLE = 2579.2242 DIHED = 812.3736
 1-4 NB = 364.0644 1-4 EEL = -563.9640 VDWAALS = 10318.3862
 EELEC = -80414.1043 EHBOND = 0.0000 RESTRAINT = -12525.2896
 EAMBER (non-restraint) = -65323.8687
 EKCMT = 6583.5570 VIRIAL = 6220.8752 VOLUME = 260397.4214
                                                    Density = 0.8383
 Ewald error estimate: 0.1108E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 200 ; vmax = 15.238182548226334
 vlimit exceeded for step 201 ; vmax = 15.144913069465751
 vlimit exceeded for step 202 ; vmax = 15.073072375371654
 vlimit exceeded for step 203 ; vmax = 15.378927755184408
 vlimit exceeded for step 207 ; vmax = 15.335680033338594
 vlimit exceeded for step 208 ; vmax = 16.582167497948699
 vlimit exceeded for step 209 ; vmax = 16.666367200277595
 vlimit exceeded for step 210 ; vmax = 15.51457074549638
 vlimit exceeded for step 247 ; vmax = 15.966848126179439
 vlimit exceeded for step 248 ; vmax = 15.729124051367757
 vlimit exceeded for step 249 ; vmax = 15.232161311446546
 vlimit exceeded for step 259 ; vmax = 15.28603135285452
 vlimit exceeded for step 260 ; vmax = 16.037787278305032
 vlimit exceeded for step 261 ; vmax = 16.083588454200868
 vlimit exceeded for step 262 ; vmax = 15.991071552671466
 vlimit exceeded for step 263 ; vmax = 15.984911292679984
 vlimit exceeded for step 264 ; vmax = 15.961421772030436
 vlimit exceeded for step 265 ; vmax = 15.944031998460275
 vlimit exceeded for step 266 ; vmax = 15.943228283738424
 vlimit exceeded for step 267 ; vmax = 15.961845941173184
 vlimit exceeded for step 268 ; vmax = 15.998150317686214
 vlimit exceeded for step 269 ; vmax = 16.046795264196358
 vlimit exceeded for step 270 ; vmax = 16.098806647646143
 vlimit exceeded for step 271 ; vmax = 16.141093867227159
 vlimit exceeded for step 272 ; vmax = 16.155115922377391
 vlimit exceeded for step 273 ; vmax = 16.115597444451609
 vlimit exceeded for step 274 ; vmax = 15.99315784838169
 vlimit exceeded for step 275 ; vmax = 15.771776556437597
 vlimit exceeded for step 276 ; vmax = 15.580601979034506
 vlimit exceeded for step 277 ; vmax = 15.625753280580028
 vlimit exceeded for step 278 ; vmax = 15.608265335005163
 vlimit exceeded for step 279 ; vmax = 15.517679458143032
 vlimit exceeded for step 280 ; vmax = 15.362290343225746
 vlimit exceeded for step 281 ; vmax = 15.182047050638147
 vlimit exceeded for step 284 ; vmax = 15.599762688437901
 vlimit exceeded for step 285 ; vmax = 15.75880012317627
 vlimit exceeded for step 298 ; vmax = 15.263204096593343
 vlimit exceeded for step 299 ; vmax = 16.54704915777792

 NSTEP = 300 TIME(PS) = 0.150 TEMP(K) = 1068.20 PRESS = 5204.0
 Etot = -63575.8590 EKtot = 45805.2839 EPtot = -109381.1429
 BOND = 3913.3056 ANGLE = 5823.8316 DIHED = 1258.1565
 1-4 NB = 613.8104 1-4 EEL = -574.1208 VDWAALS = 11218.0559
 EELEC = -79822.5080 EHBOND = 0.0000 RESTRAINT = -51811.6740
 EAMBER (non-restraint) = -57569.4689
 EKCMT = 15162.2443 VIRIAL = -14555.2135 VOLUME = 264484.1999
                                                    Density = 0.8254
 Ewald error estimate: 0.1626E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 300 ; vmax = 16.431375150534272
 vlimit exceeded for step 301 ; vmax = 16.266980225828195
 vlimit exceeded for step 302 ; vmax = 16.156623160092014
 vlimit exceeded for step 303 ; vmax = 15.889510675721569
 vlimit exceeded for step 304 ; vmax = 15.653760714867438
 vlimit exceeded for step 305 ; vmax = 17.340435997020425
 vlimit exceeded for step 306 ; vmax = 15.718210324004142
 vlimit exceeded for step 307 ; vmax = 15.113111450364654
 vlimit exceeded for step 309 ; vmax = 16.823047560485016
 vlimit exceeded for step 310 ; vmax = 16.626847276498602
 vlimit exceeded for step 311 ; vmax = 15.855128521294978
 vlimit exceeded for step 312 ; vmax = 15.525345547934224
 vlimit exceeded for step 313 ; vmax = 15.423217753442087
 vlimit exceeded for step 314 ; vmax = 15.25126814706802
 vlimit exceeded for step 317 ; vmax = 16.85714655603514
 vlimit exceeded for step 318 ; vmax = 17.917571505739225
 vlimit exceeded for step 319 ; vmax = 17.795987108684603
 vlimit exceeded for step 320 ; vmax = 18.040884179955675
 vlimit exceeded for step 321 ; vmax = 17.343841817723401
 vlimit exceeded for step 322 ; vmax = 16.720678183875922
 vlimit exceeded for step 323 ; vmax = 16.59160570781933
 vlimit exceeded for step 324 ; vmax = 16.459645503992185
 vlimit exceeded for step 325 ; vmax = 16.286885131062498
 vlimit exceeded for step 326 ; vmax = 16.139434084323852
 vlimit exceeded for step 327 ; vmax = 15.993601488908839
 vlimit exceeded for step 328 ; vmax = 15.836798215526002
 vlimit exceeded for step 329 ; vmax = 16.532838234492598
 vlimit exceeded for step 330 ; vmax = 17.156893917652432
 vlimit exceeded for step 331 ; vmax = 17.041480357466661
 vlimit exceeded for step 332 ; vmax = 16.749543146868309
 vlimit exceeded for step 333 ; vmax = 16.490886752998531
 vlimit exceeded for step 334 ; vmax = 16.284949461720299
 vlimit exceeded for step 335 ; vmax = 16.11238311119914
 vlimit exceeded for step 336 ; vmax = 15.989432372767267
 vlimit exceeded for step 337 ; vmax = 15.905602562531605
 vlimit exceeded for step 338 ; vmax = 15.753444894900372
 vlimit exceeded for step 339 ; vmax = 30.566314932451675
 vlimit exceeded for step 340 ; vmax = 17.693420239043892
 vlimit exceeded for step 341 ; vmax = 17.97646226121001
 vlimit exceeded for step 342 ; vmax = 17.529126991991259
 vlimit exceeded for step 343 ; vmax = 16.490837101594042
 vlimit exceeded for step 344 ; vmax = 15.498205511115145
 vlimit exceeded for step 345 ; vmax = 16.449761538147364
 vlimit exceeded for step 346 ; vmax = 15.893932034732844
 vlimit exceeded for step 347 ; vmax = 16.843759345914272
 vlimit exceeded for step 348 ; vmax = 18.546846824712368
 vlimit exceeded for step 349 ; vmax = 18.630289515761163
 vlimit exceeded for step 350 ; vmax = 15.945184796774111
 vlimit exceeded for step 351 ; vmax = 15.500950904957264
 vlimit exceeded for step 352 ; vmax = 15.116688807178651
 vlimit exceeded for step 353 ; vmax = 16.319765049273727
 vlimit exceeded for step 354 ; vmax = 16.585294427637798
 vlimit exceeded for step 355 ; vmax = 16.509638821497845
 vlimit exceeded for step 356 ; vmax = 16.205571481518902
 vlimit exceeded for step 357 ; vmax = 15.926169610307536
 vlimit exceeded for step 358 ; vmax = 15.696377181120528
 vlimit exceeded for step 359 ; vmax = 15.502692331904521
 vlimit exceeded for step 360 ; vmax = 15.336534855716939
 vlimit exceeded for step 361 ; vmax = 15.192423474978156
 vlimit exceeded for step 362 ; vmax = 15.060598130042797
 vlimit exceeded for step 364 ; vmax = 15.166307861392152
 vlimit exceeded for step 365 ; vmax = 16.437389409065336
 vlimit exceeded for step 366 ; vmax = 17.467443520138939
 vlimit exceeded for step 367 ; vmax = 17.618690661192769
 vlimit exceeded for step 368 ; vmax = 17.373493916785161
 vlimit exceeded for step 369 ; vmax = 16.962875926966895
 vlimit exceeded for step 370 ; vmax = 17.672341211044458
 vlimit exceeded for step 371 ; vmax = 17.087249200969829
 vlimit exceeded for step 372 ; vmax = 16.35144159756598
 vlimit exceeded for step 373 ; vmax = 16.246217316440752
 vlimit exceeded for step 374 ; vmax = 16.623212935635166
 vlimit exceeded for step 375 ; vmax = 16.033568281530496
 vlimit exceeded for step 376 ; vmax = 16.082479325692876
 vlimit exceeded for step 377 ; vmax = 15.917719200028946
 vlimit exceeded for step 378 ; vmax = 15.865624786232679
 vlimit exceeded for step 379 ; vmax = 16.250354466500955
 vlimit exceeded for step 380 ; vmax = 16.32110771945954
 vlimit exceeded for step 381 ; vmax = 16.892233010232861
 vlimit exceeded for step 382 ; vmax = 16.939268377175228
 vlimit exceeded for step 383 ; vmax = 16.737773340378276
 vlimit exceeded for step 384 ; vmax = 16.441573942186817
 vlimit exceeded for step 385 ; vmax = 15.959105057664825
 vlimit exceeded for step 386 ; vmax = 15.788998025497264
 vlimit exceeded for step 387 ; vmax = 15.478646807035934
 vlimit exceeded for step 388 ; vmax = 17.537233588339063
 vlimit exceeded for step 389 ; vmax = 15.906370071084762
 vlimit exceeded for step 390 ; vmax = 19.164420910447404
 vlimit exceeded for step 391 ; vmax = 21.834842417031478
 vlimit exceeded for step 392 ; vmax = 18.628758631455991
 vlimit exceeded for step 393 ; vmax = 16.694186304612835
 vlimit exceeded for step 394 ; vmax = 16.226576399909366
 vlimit exceeded for step 395 ; vmax = 17.131934121487166
 vlimit exceeded for step 396 ; vmax = 17.524372917690297
 vlimit exceeded for step 397 ; vmax = 17.136213787179798
 vlimit exceeded for step 398 ; vmax = 17.031334714223945
 vlimit exceeded for step 399 ; vmax = 16.869612122545533

 NSTEP = 400 TIME(PS) = 0.200 TEMP(K) = 2744.17 PRESS = 15421.8
 Etot = -88706.4949 EKtot = 117671.7941 EPtot = -206378.2890
 BOND = 10362.5215 ANGLE = 10095.6226 DIHED = 1757.7178
 1-4 NB = 755.0053 1-4 EEL = -563.0778 VDWAALS = 12223.7620
 EELEC = -73407.4557 EHBOND = 0.0000 RESTRAINT = -167602.3846
 EAMBER (non-restraint) = -38775.9044
 EKCMT = 49041.7520 VIRIAL = -48305.9212 VOLUME = 292355.7662
                                                    Density = 0.7467
 Ewald error estimate: 0.3333E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 400 ; vmax = 16.757192220893909
 vlimit exceeded for step 401 ; vmax = 16.609007494110653
 vlimit exceeded for step 402 ; vmax = 16.437526762800999
 vlimit exceeded for step 403 ; vmax = 16.271968858322978
 vlimit exceeded for step 404 ; vmax = 16.168211266982919
 vlimit exceeded for step 405 ; vmax = 16.155479095245301
 vlimit exceeded for step 406 ; vmax = 16.160197721983078
 vlimit exceeded for step 407 ; vmax = 16.17560290390843
 vlimit exceeded for step 408 ; vmax = 16.209128117050199
 vlimit exceeded for step 409 ; vmax = 16.284000603129627
 vlimit exceeded for step 410 ; vmax = 16.523070552312308
 vlimit exceeded for step 411 ; vmax = 16.531422221629906
 vlimit exceeded for step 412 ; vmax = 16.337300627137893
 vlimit exceeded for step 413 ; vmax = 16.182971605365907
 vlimit exceeded for step 414 ; vmax = 16.92006033418421
 vlimit exceeded for step 415 ; vmax = 17.572867388675519
 vlimit exceeded for step 416 ; vmax = 17.630517143436805
 vlimit exceeded for step 417 ; vmax = 17.659298429991544
 vlimit exceeded for step 418 ; vmax = 17.670456625574431
 vlimit exceeded for step 419 ; vmax = 17.663347493221085
 vlimit exceeded for step 420 ; vmax = 17.634204472864695
 vlimit exceeded for step 421 ; vmax = 17.573705937893706
 vlimit exceeded for step 422 ; vmax = 17.684231111594261
 vlimit exceeded for step 423 ; vmax = 17.437588460964125
 vlimit exceeded for step 424 ; vmax = 17.7389980446446
 vlimit exceeded for step 425 ; vmax = 17.730121525284613
 vlimit exceeded for step 426 ; vmax = 17.566575415805154
 vlimit exceeded for step 427 ; vmax = 17.354526506842923
 vlimit exceeded for step 428 ; vmax = 17.139522654150269
 vlimit exceeded for step 429 ; vmax = 16.984816681972127
 vlimit exceeded for step 430 ; vmax = 17.779381801751619
 vlimit exceeded for step 431 ; vmax = 17.308234786800675
 vlimit exceeded for step 432 ; vmax = 16.903051247765681
 vlimit exceeded for step 433 ; vmax = 16.841813520809339
 vlimit exceeded for step 434 ; vmax = 16.755681078770063
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 vlimit exceeded for step 436 ; vmax = 20.488670343528526
 vlimit exceeded for step 437 ; vmax = 18.834566311771539
 vlimit exceeded for step 438 ; vmax = 17.365598378974195
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 vlimit exceeded for step 441 ; vmax = 17.515606360105739
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 vlimit exceeded for step 444 ; vmax = 17.747665401378981
 vlimit exceeded for step 445 ; vmax = 17.261828959103855
 vlimit exceeded for step 446 ; vmax = 17.061245155022274
 vlimit exceeded for step 447 ; vmax = 17.31641081139346
 vlimit exceeded for step 448 ; vmax = 18.48017207005234
 vlimit exceeded for step 449 ; vmax = 23.867177381361486
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 vlimit exceeded for step 465 ; vmax = 17.670277718903705
 vlimit exceeded for step 466 ; vmax = 18.112039702300958
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 vlimit exceeded for step 468 ; vmax = 18.225795916790396
 vlimit exceeded for step 469 ; vmax = 18.133029836921079
 vlimit exceeded for step 470 ; vmax = 17.931018367550763
 vlimit exceeded for step 471 ; vmax = 17.772286260439355
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 vlimit exceeded for step 474 ; vmax = 18.400577601636385
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 vlimit exceeded for step 485 ; vmax = 18.232283345356922
 vlimit exceeded for step 486 ; vmax = 18.129273085206822
 vlimit exceeded for step 487 ; vmax = 18.048984014808088
 vlimit exceeded for step 488 ; vmax = 18.007585952513633
 vlimit exceeded for step 489 ; vmax = 18.184146137831288
 vlimit exceeded for step 490 ; vmax = 18.273015592909548
 vlimit exceeded for step 491 ; vmax = 23.129994393786831
 vlimit exceeded for step 492 ; vmax = 19.047160110216549
 vlimit exceeded for step 493 ; vmax = 18.426723455279891
 vlimit exceeded for step 494 ; vmax = 18.513651479534811
 vlimit exceeded for step 495 ; vmax = 18.596507940835014
 vlimit exceeded for step 496 ; vmax = 18.681726904149599
 vlimit exceeded for step 497 ; vmax = 18.778036375006881
 vlimit exceeded for step 498 ; vmax = 21.05751632452554
 vlimit exceeded for step 499 ; vmax = 25.48250365183555

 NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 7443.57 PRESS = 27280.8
 Etot = -223066.1603 EKtot = 319184.9509 EPtot = -542251.1113
 BOND = 28654.6722 ANGLE = 17346.2653 DIHED = 2434.3908
 1-4 NB = 1525.2266 1-4 EEL = -835.4973 VDWAALS = 11697.4899
 EELEC = -57788.7151 EHBOND = 0.0000 RESTRAINT = -545284.9439
 EAMBER (non-restraint) = 3033.8326
 EKCMT = 139379.0545 VIRIAL = -82567.6209 VOLUME = 376802.3496
                                                    Density = 0.5793
 Ewald error estimate: 0.2833E-04
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
 vlimit exceeded for step 500 ; vmax = 23.779691776878693
 vlimit exceeded for step 501 ; vmax = 20.450180488514221
 vlimit exceeded for step 502 ; vmax = 19.198469627802883
 vlimit exceeded for step 503 ; vmax = 18.576364994946506
 vlimit exceeded for step 504 ; vmax = 18.673911889833988
 vlimit exceeded for step 505 ; vmax = 18.795352977205592
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 vlimit exceeded for step 508 ; vmax = 18.80677009495486
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 vlimit exceeded for step 512 ; vmax = 19.073667726909971
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 vlimit exceeded for step 519 ; vmax = 18.41822702833289
 vlimit exceeded for step 520 ; vmax = 18.218140180463458
 vlimit exceeded for step 521 ; vmax = 18.808125428048452
 vlimit exceeded for step 522 ; vmax = 19.470347010012663
 vlimit exceeded for step 523 ; vmax = 19.165267681564774
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 vlimit exceeded for step 525 ; vmax = 19.846996192659383
 vlimit exceeded for step 526 ; vmax = 19.491521861154105
 vlimit exceeded for step 527 ; vmax = 19.179387037915955
 vlimit exceeded for step 528 ; vmax = 22.79822781066504
 vlimit exceeded for step 529 ; vmax = 26.066898819689612
 vlimit exceeded for step 530 ; vmax = 22.356130345214233
 vlimit exceeded for step 531 ; vmax = 18.691677963054254
 vlimit exceeded for step 532 ; vmax = 18.4279640162341
 vlimit exceeded for step 533 ; vmax = 18.455893789440076
 vlimit exceeded for step 534 ; vmax = 19.44872156674284
 vlimit exceeded for step 535 ; vmax = 22.026922898339993
 vlimit exceeded for step 536 ; vmax = 24.140670106036747
 vlimit exceeded for step 537 ; vmax = 23.130656985081771
 vlimit exceeded for step 538 ; vmax = 23.880954747436345
 vlimit exceeded for step 539 ; vmax = 24.268707324372002
 SANDER BOMB in subroutine nonbond_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander

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Received on Wed Jun 16 2004 - 15:53:01 PDT
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