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
>
>
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | Run on 10/02/2010 at 11:19:15
> [-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,
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sat Oct 02 2010 - 06:00:03 PDT
