Hi,
I don't know why, but now it works, also with the crgmask.
I use the following command to start the job:
qsub -q long.q -e err1 -o out1 -cwd -pe orte
2 ./s3_m17_l1_dna_calculations_dna.bash
Thank yo for your help.
Kind Regards,
Kirsten
the outputfile looks now:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 10/03/2010 at 15:41:00
[-O]verwriting output
File Assignments:
| MDIN:
mdin_min_s3_v0_l1_dna
| MDOUT:
m17_min_s3_v0_l1_dna.out
|INPCRD:
m17_dna.rst
| PARM:
m17_dna.prm
|RESTRT:
m17_min_s3_v0_l1_dna.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
| MTMD:
mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
density
minlibration
&cntrl
imin = 1, ntx =
1,
maxcyc = 500, nstlim =
10,
ntpr =
100,
ntf = 1, ntc =
1,
ntb = 1, cut =
12.0,
icfe = 1, clambda =
0.1,
ifsc=0,
crgmask =
':1,10,11,20',
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 33.148
| New format PARM file being parsed.
| Version = 1.000 Date = 08/27/10 Time = 21:10:37
NATOM = 16269 NTYPES = 19 NBONH = 15809 MBONA = 452
NTHETH = 542 MTHETA = 694 NPHIH = 1150 MPHIA = 1230
NHPARM = 0 NPARM = 0 NNB = 24348 NRES = 5269
NBONA = 452 NTHETA = 694 NPHIA = 1230 NUMBND = 39
NUMANG = 76 NPTRA = 42 NATYP = 29 NPHB = 1
IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1108294
| Hollerith 54078
| Integer 490972
| Max Pairs 14880712
| nblistReal 195228
| nblist Int 731425
| Total 73297 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
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 = 0, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 500, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Free energy options:
icfe = 1, ifsc = 0, klambda = 1
clambda = 0.1000, scalpha = 0.5000, scbeta = 12.0000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 66.296 Box Y = 75.263 Box Z = 77.486
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 75 NFFT3 = 80
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
Zero-Charge Mask :1,10,11,20; matches 126 atoms
Removing charge of 0.4422 from atom 1
Removing charge of -0.6318 from atom 2
Removing charge of -0.0069 from atom 3
Removing charge of 0.0754 from atom 4
Removing charge of 0.0754 from atom 5
Removing charge of 0.1629 from atom 6
Removing charge of 0.1176 from atom 7
Removing charge of -0.3691 from atom 8
Removing charge of 0.0680 from atom 9
Removing charge of 0.1804 from atom 10
Removing charge of -0.0239 from atom 11
Removing charge of -0.2209 from atom 12
Removing charge of 0.2607 from atom 13
Removing charge of 0.0025 from atom 14
Removing charge of -0.2269 from atom 15
Removing charge of 0.0770 from atom 16
Removing charge of 0.0770 from atom 17
Removing charge of 0.0770 from atom 18
Removing charge of 0.5194 from atom 19
Removing charge of -0.5563 from atom 20
Removing charge of -0.4340 from atom 21
Removing charge of 0.3420 from atom 22
Removing charge of 0.5677 from atom 23
Removing charge of -0.5881 from atom 24
Removing charge of 0.0713 from atom 25
Removing charge of 0.0985 from atom 26
Removing charge of -0.0854 from atom 27
Removing charge of 0.0718 from atom 28
Removing charge of 0.0718 from atom 29
Removing charge of -0.5232 from atom 30
Removing charge of 1.1659 from atom 285
Removing charge of -0.7761 from atom 286
Removing charge of -0.7761 from atom 287
Removing charge of -0.4954 from atom 288
Removing charge of -0.0069 from atom 289
Removing charge of 0.0754 from atom 290
Removing charge of 0.0754 from atom 291
Removing charge of 0.1629 from atom 292
Removing charge of 0.1176 from atom 293
Removing charge of -0.3691 from atom 294
Removing charge of 0.0680 from atom 295
Removing charge of 0.1804 from atom 296
Removing charge of -0.0239 from atom 297
Removing charge of -0.2209 from atom 298
Removing charge of 0.2607 from atom 299
Removing charge of 0.0025 from atom 300
Removing charge of -0.2269 from atom 301
Removing charge of 0.0770 from atom 302
Removing charge of 0.0770 from atom 303
Removing charge of 0.0770 from atom 304
Removing charge of 0.5194 from atom 305
Removing charge of -0.5563 from atom 306
Removing charge of -0.4340 from atom 307
Removing charge of 0.3420 from atom 308
Removing charge of 0.5677 from atom 309
Removing charge of -0.5881 from atom 310
Removing charge of 0.0713 from atom 311
Removing charge of 0.0985 from atom 312
Removing charge of -0.0854 from atom 313
Removing charge of 0.0718 from atom 314
Removing charge of 0.0718 from atom 315
Removing charge of -0.6549 from atom 316
Removing charge of 0.4396 from atom 317
Removing charge of 0.4422 from atom 318
Removing charge of -0.6318 from atom 319
Removing charge of -0.0069 from atom 320
Removing charge of 0.0754 from atom 321
Removing charge of 0.0754 from atom 322
Removing charge of 0.1629 from atom 323
Removing charge of 0.1176 from atom 324
Removing charge of -0.3691 from atom 325
Removing charge of 0.0431 from atom 326
Removing charge of 0.1838 from atom 327
Removing charge of -0.0268 from atom 328
Removing charge of 0.1607 from atom 329
Removing charge of 0.1877 from atom 330
Removing charge of -0.6175 from atom 331
Removing charge of 0.0725 from atom 332
Removing charge of 0.6897 from atom 333
Removing charge of -0.9123 from atom 334
Removing charge of 0.4167 from atom 335
Removing charge of 0.4167 from atom 336
Removing charge of -0.7624 from atom 337
Removing charge of 0.5716 from atom 338
Removing charge of 0.0598 from atom 339
Removing charge of -0.7417 from atom 340
Removing charge of 0.3800 from atom 341
Removing charge of 0.0713 from atom 342
Removing charge of 0.0985 from atom 343
Removing charge of -0.0854 from atom 344
Removing charge of 0.0718 from atom 345
Removing charge of 0.0718 from atom 346
Removing charge of -0.5232 from atom 347
Removing charge of 1.1659 from atom 602
Removing charge of -0.7761 from atom 603
Removing charge of -0.7761 from atom 604
Removing charge of -0.4954 from atom 605
Removing charge of -0.0069 from atom 606
Removing charge of 0.0754 from atom 607
Removing charge of 0.0754 from atom 608
Removing charge of 0.1629 from atom 609
Removing charge of 0.1176 from atom 610
Removing charge of -0.3691 from atom 611
Removing charge of 0.0431 from atom 612
Removing charge of 0.1838 from atom 613
Removing charge of -0.0268 from atom 614
Removing charge of 0.1607 from atom 615
Removing charge of 0.1877 from atom 616
Removing charge of -0.6175 from atom 617
Removing charge of 0.0725 from atom 618
Removing charge of 0.6897 from atom 619
Removing charge of -0.9123 from atom 620
Removing charge of 0.4167 from atom 621
Removing charge of 0.4167 from atom 622
Removing charge of -0.7624 from atom 623
Removing charge of 0.5716 from atom 624
Removing charge of 0.0598 from atom 625
Removing charge of -0.7417 from atom 626
Removing charge of 0.3800 from atom 627
Removing charge of 0.0713 from atom 628
Removing charge of 0.0985 from atom 629
Removing charge of -0.0854 from atom 630
Removing charge of 0.0718 from atom 631
Removing charge of 0.0718 from atom 632
Removing charge of -0.6549 from atom 633
Removing charge of 0.4396 from atom 634
Total charge of -2.0000 removed
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 5193
| Atom division among processors:
| 0 16269
Sum of charges from parm topology file = 2.00000009
Assuming uniform neutralizing plasma
| Running AMBER/MPI version on 1 nodes
| MULTISANDER: 2 groups. 1 processors out of 2 total.
--------------------------------------------------------------------------------
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 = 0.7967E-11 at 2.716640
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6742675
| TOTAL SIZE OF NONBOND LIST = 6742675
NSTEP ENERGY RMS GMAX NAME
NUMBER
1 1.8123E+04 4.6044E+03 5.2067E+05 O 6295
BOND = 5064.4778 ANGLE = 303.5109 DIHED =
384.5016
VDWAALS = 101276.9345 EEL = -87398.4163 HBOND =
0.0000
1-4 VDW = 166.4912 1-4 EEL = -1674.6544 RESTRAINT =
0.0000
DV/DL = -678.7860
NSTEP ENERGY RMS GMAX NAME
NUMBER
100 -7.1294E+04 6.2654E-01 2.9708E+01 C1' 295
BOND = 4954.3210 ANGLE = 107.0430 DIHED =
378.2515
VDWAALS = 13039.5460 EEL = -88251.0478 HBOND =
0.0000
1-4 VDW = 151.5539 1-4 EEL = -1673.7070 RESTRAINT =
0.0000
DV/DL = -556.6152
NSTEP ENERGY RMS GMAX NAME
NUMBER
200 -7.1655E+04 3.4208E-01 1.6795E+01 C5 300
BOND = 5024.2192 ANGLE = 98.1201 DIHED =
372.7803
VDWAALS = 13450.5383 EEL = -89080.6962 HBOND =
0.0000
1-4 VDW = 147.4398 1-4 EEL = -1667.6979 RESTRAINT =
0.0000
DV/DL = -538.8399
NSTEP ENERGY RMS GMAX NAME
NUMBER
300 -7.1877E+04 2.9271E-01 1.2397E+01 C6 298
BOND = 5068.6257 ANGLE = 93.6204 DIHED =
374.4700
VDWAALS = 13651.6544 EEL = -89546.5627 HBOND =
0.0000
1-4 VDW = 146.7336 1-4 EEL = -1665.0883 RESTRAINT =
0.0000
DV/DL = -538.1047
NSTEP ENERGY RMS GMAX NAME
NUMBER
400 -7.2104E+04 2.8933E-01 1.2337E+01 C6 298
BOND = 5116.6582 ANGLE = 91.5443 DIHED =
377.1387
VDWAALS = 13877.2887 EEL = -90048.9107 HBOND =
0.0000
1-4 VDW = 146.0485 1-4 EEL = -1663.4863 RESTRAINT =
0.0000
DV/DL = -536.1866
NSTEP ENERGY RMS GMAX NAME
NUMBER
500 -7.2219E+04 3.1184E-01 9.6659E+00 C2' 313
BOND = 5140.3022 ANGLE = 90.1322 DIHED =
378.5854
VDWAALS = 13991.7770 EEL = -90302.9212 HBOND =
0.0000
1-4 VDW = 146.0218 1-4 EEL = -1662.9525 RESTRAINT =
0.0000
DV/DL = -534.9803
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME
NUMBER
500 -7.2219E+04 3.1184E-01 9.6659E+00 C2' 313
BOND = 5140.3022 ANGLE = 90.1322 DIHED =
378.5854
VDWAALS = 13991.7770 EEL = -90302.9212 HBOND =
0.0000
1-4 VDW = 146.0218 1-4 EEL = -1662.9525 RESTRAINT =
0.0000
DV/DL = -534.9803
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.05 ( 0.01% of Total)
| Build the list 3.39 (96.41% of List )
| Other 0.13 ( 3.59% of List )
| List time 3.52 ( 1.06% of Nonbo)
| Short_ene time 272.25 (99.55% of Direc)
| Other 1.24 ( 0.45% of Direc)
| Direct Ewald time 273.49 (83.50% of Ewald)
| Adjust Ewald time 0.92 ( 0.28% of Ewald)
| Fill Bspline coeffs 1.41 ( 2.67% of Recip)
| Fill charge grid 4.78 ( 9.05% of Recip)
| Scalar sum 18.29 (34.60% of Recip)
| Grad sum 6.92 (13.09% of Recip)
| FFT time 21.45 (40.59% of Recip)
| Other 0.01 ( 0.01% of Recip)
| Recip Ewald time 52.85 (16.14% of Ewald)
| Virial junk 0.19 ( 0.06% of Ewald)
| Other 0.06 ( 0.02% of Ewald)
| Ewald time 327.52 (98.94% of Nonbo)
| Nonbond force 331.04 (99.68% of Force)
| Bond/Angle/Dihedral 1.01 ( 0.31% of Force)
| Other 0.04 ( 0.01% of Force)
| Force time 332.10 (100.0% of Runmd)
| Runmd Time 332.10 (95.74% of Total)
| Other 14.72 ( 4.24% of Total)
| Total time 346.87 (100.0% of ALL )
| Highest rstack allocated: 1357725
| Highest istack allocated: 16269
| Job began at 15:41:00.113 on 10/03/2010
| Setup done at 15:41:00.355 on 10/03/2010
| Run done at 15:46:46.982 on 10/03/2010
| wallclock() was called 22065 times
Am Samstag, den 02.10.2010, 08:44 -0400 schrieb
steinbrt.rci.rutgers.edu:
> Hi,
>
> could you try the following:
>
> Try and run the calculation with nstlim=10 while removing the crgmask
> command from V0 (This will give you a DVDL of 0, but it's just for
> debugging...). If it runs through, please send the command that you used
> (e.g. your pbs script) and both mdout files to the list. Maybe we'll be
> able to spot something then.
>
> Kind Regards,
>
> Thomas
> On Sat, October 2, 2010 5:30 am, Kirsten Heitmann wrote:
> > Am Freitag, den 01.10.2010, 16:40 -0400 schrieb Jason Swails:
> >> Hello,
> >>
> >> When you use ntc=1, try also using ntf=1. ntc restrains the bond
> >> lengths,
> >> but by setting ntf=2, you are omitting all force calculations involving
> >> hydrogens (bonded force calculations, that is, obviously the non-bonded
> >> ones
> >> are still executed).
> >>
> >> Hope this helps,
> >> Jason
> >>
> >
> > Hi,
> >
> > this is the output, when I set ntc= 1 and ntf=1,
> > it stops at the same position like before.
> >
> > Kind Regards,
> > Kirsten
> >
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Received on Mon Oct 04 2010 - 03:30:03 PDT
