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
vlimit exceeded for step 435 ; vmax = 18.861040241072232
vlimit exceeded for step 436 ; vmax = 20.488670343528526
vlimit exceeded for step 437 ; vmax = 18.834566311771539
vlimit exceeded for step 438 ; vmax = 17.365598378974195
vlimit exceeded for step 439 ; vmax = 17.363790805378173
vlimit exceeded for step 440 ; vmax = 17.53135333643845
vlimit exceeded for step 441 ; vmax = 17.515606360105739
vlimit exceeded for step 442 ; vmax = 17.452676379324647
vlimit exceeded for step 443 ; vmax = 17.944612262073633
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
vlimit exceeded for step 450 ; vmax = 19.73055701078567
vlimit exceeded for step 451 ; vmax = 19.318467973559109
vlimit exceeded for step 452 ; vmax = 18.044096356615455
vlimit exceeded for step 453 ; vmax = 18.246492385488494
vlimit exceeded for step 454 ; vmax = 19.095095321212479
vlimit exceeded for step 455 ; vmax = 19.459761245649382
vlimit exceeded for step 456 ; vmax = 19.317230661530601
vlimit exceeded for step 457 ; vmax = 18.771351889752552
vlimit exceeded for step 458 ; vmax = 18.045775210894757
vlimit exceeded for step 459 ; vmax = 17.509890168253254
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vlimit exceeded for step 461 ; vmax = 17.218802859045564
vlimit exceeded for step 462 ; vmax = 17.360376414361706
vlimit exceeded for step 463 ; vmax = 17.47140385017261
vlimit exceeded for step 464 ; vmax = 17.521532447660189
vlimit exceeded for step 465 ; vmax = 17.670277718903705
vlimit exceeded for step 466 ; vmax = 18.112039702300958
vlimit exceeded for step 467 ; vmax = 17.911832260187996
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
vlimit exceeded for step 472 ; vmax = 17.599319550210989
vlimit exceeded for step 473 ; vmax = 17.967961530646537
vlimit exceeded for step 474 ; vmax = 18.400577601636385
vlimit exceeded for step 475 ; vmax = 20.894739982824365
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vlimit exceeded for step 478 ; vmax = 19.371801179369946
vlimit exceeded for step 479 ; vmax = 17.870003063731236
vlimit exceeded for step 480 ; vmax = 17.812491035164228
vlimit exceeded for step 481 ; vmax = 17.982348066038192
vlimit exceeded for step 482 ; vmax = 20.35030812959576
vlimit exceeded for step 483 ; vmax = 21.813695594667262
vlimit exceeded for step 484 ; vmax = 20.317284200281634
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
vlimit exceeded for step 506 ; vmax = 18.851642787625934
vlimit exceeded for step 507 ; vmax = 18.852315189310136
vlimit exceeded for step 508 ; vmax = 18.80677009495486
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vlimit exceeded for step 510 ; vmax = 18.683689510561088
vlimit exceeded for step 511 ; vmax = 18.903606600166558
vlimit exceeded for step 512 ; vmax = 19.073667726909971
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vlimit exceeded for step 514 ; vmax = 19.141642174013498
vlimit exceeded for step 515 ; vmax = 19.046942273282493
vlimit exceeded for step 516 ; vmax = 20.952438514963326
vlimit exceeded for step 517 ; vmax = 21.351704135100775
vlimit exceeded for step 518 ; vmax = 19.824738749558858
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
vlimit exceeded for step 524 ; vmax = 20.003087138093822
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
