AMBER Archive (2005)

Subject: Re: AMBER: question about TGMD: vlimit exceeded for step

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Fri Apr 08 2005 - 15:47:40 CDT

I think your masks are reversed. According to your input you overlap
your molecule to a reference by residues 81-86 and calculate the force
based on RMSD of residues 3-122. You should try to switch the masks,
such as: tgtfitmask=':3-122', tgtrmsmask=':81-86 & !@H=', or use
positional restraints (ntr=1) for atoms :3-80,87-122
(restraintmask=':3-80,87-122', restraint_wt = 2.0, or such) and use
targeted md for :81-86 (tgtrmsmask=':81-86')...

Cheers,
-Viktor

xhu1_at_memphis.edu wrote:

>Dear all,
>
>I am trying to run TGMD for a system: a 124-residue protein in a
>waterbox.
>
>Using AMBER7, weighted TGTRMSD from 4.345 to 0, TGTMDMDFRC=10 or 5 or
>1, restrain force applied on residue 3-122, job running OK. then I
>tried to apply the restraint force on residue 81-86 only, to see if
>the structure will go to the reference structure as well. AMBER7 seems
>not be able to do this. I move to AMBER8. Here is the input file:
>*****************************************************************
>#Data collection at 298K
> &cntrl
> IMIN = 0,ntx=5,irest=1,
> ntpr=10, ntwr=500,
> ntb=1,ntr=0,
> ntf=2,ntc=2,
> cut=8.5, nscm = 1000,
> NSTLIM = 400000, DT = 0.002,
> NTWX=500, NTWV=500,NTWE=500,
> TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
> nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=10.00,
> tgtrmsmask=":3-122", tgtfitmask=":81-86 & !@H=",
> &end
> &wt
> TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
> value1 = 4.345, value2 = 0.3,
> &end
> &wt
> TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
> value1 = 0.3, value2 = 0.,
> &end
> &wt
> type="END",
> &end
> &rst
> iat(1)=0,
> &end
>END
>***********************************************************************
>
>I got a problem: job stopped immediately, and gave the informatin as
>following:
>
>*********************************************
>
> NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 5403.88 PRESS
>= 0.0
> Etot = 867849.0298 EKtot = 181470.7791 EPtot =
>686378.2507
> BOND = 1342.9958 ANGLE = 1534.9087 DIHED =
>1235.1722
> 1-4 NB = 1138.3272 1-4 EEL = 5449.3066 VDWAALS =
>9292.6310
> EELEC = -64101.8524 EHBOND = 0.0000 RESTRAINT =
>730486.7616
> EAMBER (non-restraint) = -44108.5108
> Ewald error estimate: 0.2247E-04
>Current RMSD from reference: 13.246
>Current target RMSD: 4.345
> ----------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>0.000
>=======================================================================
> vlimit exceeded for step 11 ; vmax = 21.4771801052079
> vlimit exceeded for step 12 ; vmax = 1952.41027295489
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 439 882 883
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>***********************************************************************
>
>I noticed that the "Current RMSD from reference" is huge different
>from the "Current target RMSD". Is my TGTMDFRC too large?? I decreased
>this value to 5, then 1, after running several tens steps, jobs
>stopped for the same reason too. I read some emails in the mailing
>list. the value of TGTMDFRC between 1-5 or 1-10 should be OK. then
>does my input file have a problem?
>
>Thank you very much for your help!
>
>Shawn
>
>
>------------------------------------------------------------------------
>
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
>| Run on 04/08/2005 at 14:36:53
> [-O]verwriting output
>
>File Assignments:
>| MDIN: NVTTGMDdata-f1-new2-8186.in
>| MDOUT: NVTTGMDdata-f1-new2-8186.out
>|INPCRD: ../NVTMD8.rst
>| PARM: ../ntrc.parm
>|RESTRT: NVTTGMDdata-f1-new2-8186.rst
>| REFC: ../ref-pntrc2-final.rst
>| MDVEL: mdvel
>| MDEN: mden
>| MDCRD: NVTTGMDdata-f1-new2-8186.dat
>|MDINFO: mdinfo
>|INPDIP: inpdip
>|RSTDIP: rstdip
>
>
> Here is the input file:
>
>#Data collection at 298K
> &cntrl
> IMIN = 0,ntx=5,irest=1,
> ntpr=10, ntwr=500,
> ntb=1,ntr=0,
> ntf=2,ntc=2,
> cut=8.5, nscm = 1000,
> NSTLIM = 400000, DT = 0.002,
> NTWX=500, NTWV=500,NTWE=500,
> TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
> nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=1.00,
> tgtrmsmask=":3-122", tgtfitmask=":81-86 & !@H=",
> &end
> &wt
> TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
> value1 = 4.345, value2 = 0.3,
> &end
> &wt
> TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
> value1 = 0.3, value2 = 0.,
> &end
> &wt
> type="END",
> &end
> &rst
> iat(1)=0,
> &end
>END
>
>
>--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>--------------------------------------------------------------------------------
>
>| Flags:
> getting new box info from bottom of inpcrd
>| peek_ewald_inpcrd: Box info found
>|Largest sphere to fit in unit cell has radius = 24.383
>| New format PARM file being parsed.
>| Version = 1.000 Date = 05/11/04 Time = 13:47:55
> NATOM = 16419 NTYPES = 17 NBONH = 15456 MBONA = 974
> NTHETH = 2179 MTHETA = 1325 NPHIH = 4033 MPHIA = 2476
> NHPARM = 0 NPARM = 0 NNB = 29899 NRES = 4964
> NBONA = 974 NTHETA = 1325 NPHIA = 2476 NUMBND = 45
> NUMANG = 91 NPTRA = 40 NATYP = 32 NPHB = 1
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
>| Memory Use Allocated
>| Real 1226108
>| Hollerith 103480
>| Integer 1117705
>| Max Pairs 6335681
>| Max Rstack 932238
>| Max Istack 82095
>| Total 46701 kbytes
>| Duplicated 0 dihedrals
>| Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
>--------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>--------------------------------------------------------------------------------
>
>
>
>General flags:
> imin = 0, nmropt = 1
>
>Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
>
>Nature and format of output:
> ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 500
> iwrap = 0, ntwx = 500, ntwv = 500, ntwe = 500
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>
>Potential function:
> ntf = 2, ntb = 1, igb = 0, nsnb = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 8.50000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
>Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
>Molecular dynamics:
> nstlim = 400000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>
>Berendsen (weak-coupling) temperature regulation:
> temp0 = 298.00000, tempi = 298.00000, tautp = 2.00000
>
>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
>
>Targeted molecular dynamics:
> tgtrmsd = 4.34500, tgtmdfrc= 1.00000
>
>Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 59.725 Box Y = 59.725 Box Z = 59.725
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 60 NFFT2 = 60 NFFT3 = 60
> Cutoff= 8.500 Tol =0.100E-04
> Ewald Coefficient = 0.32692
> Interpolation order = 4
>
> LOADING THE TARGETED MD ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> Mask ":81-86 & !@H=" matches 44 atoms
> Mask ":3-122" matches 1844 atoms
>
>--------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>--------------------------------------------------------------------------------
>
>
> begin time read from input coords = 360.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TGTRMSD 0 200000 4.345000 0.300000 0 0
> TGTRMSD 200001 400000 0.300000 0.000000 0 0
>
> RESTRAINTS:
> No valid redirection requests found
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 4833
>
> 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 = 0.2738E-14 at 2.422500
>| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
>| Local SIZE OF NONBOND LIST = 3955885
>| TOTAL SIZE OF NONBOND LIST = 3955885
>
> NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 355.07 PRESS = 0.0
> Etot = 50500.3752 EKtot = 11923.7546 EPtot = 38576.6206
> BOND = 346.8263 ANGLE = 987.1127 DIHED = 1189.6780
> 1-4 NB = 485.3643 1-4 EEL = 5256.5550 VDWAALS = 5689.6013
> EELEC = -64209.2727 EHBOND = 0.0000 RESTRAINT = 88830.7558
> EAMBER (non-restraint) = -50254.1352
> Ewald error estimate: 0.4247E-04
>Current RMSD from reference: 14.160
>Current target RMSD: 4.345
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 20 TIME(PS) = 360.040 TEMP(K) = 513.04 PRESS = 0.0
> Etot = 49794.4326 EKtot = 17228.8291 EPtot = 32565.6035
> BOND = 360.2052 ANGLE = 996.3310 DIHED = 1175.6930
> 1-4 NB = 566.4743 1-4 EEL = 5333.5054 VDWAALS = 5881.2507
> EELEC = -64152.7900 EHBOND = 0.0000 RESTRAINT = 82404.9339
> EAMBER (non-restraint) = -49839.3305
> Ewald error estimate: 0.5287E-04
>Current RMSD from reference: 13.799
>Current target RMSD: 4.345
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 30 TIME(PS) = 360.060 TEMP(K) = 733.56 PRESS = 0.0
> Etot = 49568.1573 EKtot = 24634.1062 EPtot = 24934.0511
> BOND = 433.7839 ANGLE = 1100.1413 DIHED = 1211.9403
> 1-4 NB = 681.9878 1-4 EEL = 5418.3869 VDWAALS = 6474.5780
> EELEC = -64128.7313 EHBOND = 0.0000 RESTRAINT = 73741.9641
> EAMBER (non-restraint) = -48807.9131
> Ewald error estimate: 0.1075E-03
>Current RMSD from reference: 13.288
>Current target RMSD: 4.344
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 40 TIME(PS) = 360.080 TEMP(K) = 985.39 PRESS = 0.0
> Etot = 50738.3463 EKtot = 33091.0901 EPtot = 17647.2562
> BOND = 509.7100 ANGLE = 1351.2235 DIHED = 1288.5195
> 1-4 NB = 786.7035 1-4 EEL = 5432.4635 VDWAALS = 7447.8058
> EELEC = -64042.5993 EHBOND = 0.0000 RESTRAINT = 64873.4298
> EAMBER (non-restraint) = -47226.1736
> Ewald error estimate: 0.1783E-03
>Current RMSD from reference: 12.732
>Current target RMSD: 4.344
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 50 TIME(PS) = 360.100 TEMP(K) = 1267.52 PRESS = 0.0
> Etot = 53721.7960 EKtot = 42565.3549 EPtot = 11156.4411
> BOND = 563.8761 ANGLE = 1601.7784 DIHED = 1412.4925
> 1-4 NB = 824.8131 1-4 EEL = 5477.7329 VDWAALS = 8342.6842
> EELEC = -64000.0255 EHBOND = 0.0000 RESTRAINT = 56933.0894
> EAMBER (non-restraint) = -45776.6483
> Ewald error estimate: 0.8878E-04
>Current RMSD from reference: 12.202
>Current target RMSD: 4.344
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 60 TIME(PS) = 360.120 TEMP(K) = 1560.11 PRESS = 0.0
> Etot = 57067.4661 EKtot = 52390.8133 EPtot = 4676.6528
> BOND = 681.2052 ANGLE = 1932.4337 DIHED = 1575.3324
> 1-4 NB = 879.3654 1-4 EEL = 5487.3101 VDWAALS = 8810.9370
> EELEC = -63642.5994 EHBOND = 0.0000 RESTRAINT = 48952.6684
> EAMBER (non-restraint) = -44276.0156
> Ewald error estimate: 0.6832E-04
>Current RMSD from reference: 11.630
>Current target RMSD: 4.344
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 70 TIME(PS) = 360.140 TEMP(K) = 1841.89 PRESS = 0.0
> Etot = 60565.8429 EKtot = 61853.5428 EPtot = -1287.6999
> BOND = 708.4722 ANGLE = 2331.4137 DIHED = 1774.3048
> 1-4 NB = 958.5900 1-4 EEL = 5515.1071 VDWAALS = 9612.3293
> EELEC = -63380.1996 EHBOND = 0.0000 RESTRAINT = 41192.2826
> EAMBER (non-restraint) = -42479.9825
> Ewald error estimate: 0.7494E-04
>Current RMSD from reference: 11.028
>Current target RMSD: 4.344
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 80 TIME(PS) = 360.160 TEMP(K) = 2123.51 PRESS = 0.0
> Etot = 63443.4594 EKtot = 71310.7022 EPtot = -7867.2428
> BOND = 843.3182 ANGLE = 2794.2482 DIHED = 1801.5359
> 1-4 NB = 1012.3003 1-4 EEL = 5375.9983 VDWAALS = 9907.3753
> EELEC = -62895.9791 EHBOND = 0.0000 RESTRAINT = 33293.9601
> EAMBER (non-restraint) = -41161.2029
> Ewald error estimate: 0.1824E-03
>Current RMSD from reference: 10.353
>Current target RMSD: 4.343
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 90 TIME(PS) = 360.180 TEMP(K) = 2372.33 PRESS = 0.0
> Etot = 66114.2544 EKtot = 79666.6235 EPtot = -13552.3691
> BOND = 869.8000 ANGLE = 3308.4719 DIHED = 1954.7919
> 1-4 NB = 993.1820 1-4 EEL = 5253.8136 VDWAALS = 10605.0434
> EELEC = -62737.9688 EHBOND = 0.0000 RESTRAINT = 26200.4969
> EAMBER (non-restraint) = -39752.8660
> Ewald error estimate: 0.1640E-03
>Current RMSD from reference: 9.674
>Current target RMSD: 4.343
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 100 TIME(PS) = 360.200 TEMP(K) = 2590.63 PRESS = 0.0
> Etot = 69428.3759 EKtot = 86997.3026 EPtot = -17568.9267
> BOND = 979.3832 ANGLE = 3623.9207 DIHED = 2086.0821
> 1-4 NB = 899.4468 1-4 EEL = 5075.9477 VDWAALS = 11098.2017
> EELEC = -62235.3361 EHBOND = 0.0000 RESTRAINT = 20903.4272
> EAMBER (non-restraint) = -38472.3539
> Ewald error estimate: 0.1686E-03
>Current RMSD from reference: 9.104
>Current target RMSD: 4.343
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 110 TIME(PS) = 360.220 TEMP(K) = 2778.98 PRESS = 0.0
> Etot = 73334.1524 EKtot = 93322.6000 EPtot = -19988.4477
> BOND = 1104.6016 ANGLE = 3787.9171 DIHED = 2094.1585
> 1-4 NB = 915.1784 1-4 EEL = 5008.0793 VDWAALS = 11633.5499
> EELEC = -61807.7074 EHBOND = 0.0000 RESTRAINT = 17275.7749
> EAMBER (non-restraint) = -37264.2226
> Ewald error estimate: 0.2759E-03
>Current RMSD from reference: 8.671
>Current target RMSD: 4.343
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
> vlimit exceeded for step 119 ; vmax = 28.1889953257862
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 274 553 554
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>

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