AMBER Archive (2009)

Subject: Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala

From: Wallace Kunin (kunin_at_marshall.edu)
Date: Tue Nov 17 2009 - 09:20:13 CST

This is Run.tgtmd in the $AMBERHOME/test/tgtmd/change_target.ntr directory

> #!/bin/csh -f
>
> echo "SANDER: Targeted MD with changing target and restraints"
>
> if( ! $?TESTsander ) then
> set sander = "../../../exe/sander"
> else
> set sander = "$TESTsander"
> endif
>
> if( ! $?DO_PARALLEL ) then
> setenv DO_PARALLEL " "
> else
> set numprocs=`echo $DO_PARALLEL | awk -f ../../numprocs.awk `
> if ( $numprocs > 2 ) then
> echo " DO_PARALLEL set to $DO_PARALLEL"
> goto toomany
> else if ( $?MP_PROCS)then
> if ($MP_PROCS > 2)then
> # --- For IBM AIX ---
> echo " MP_PROCS set to "$MP_PROCS
> goto toomany
> endif
> endif
> endif
>
> touch dummy
> $DO_PARALLEL $sander \
> -O \
> -i tgtmd.in \
> -o tgtmd.out \
> -p prmtop \
> -c inpcrd \
> -ref refcrd \
> -x tgtmd.trj \
> -inf tgtmd.info \
> -r tgtmd.restrt < dummy || goto error
>
>
> ../../dacdif tgtmd.out.save tgtmd.out
> /bin/rm -f tgtmd.trj tgtmd.info tgtmd.restrt dummy
> exit(0)
>
> error:
> echo " ${0}: Program error"
> exit(1)
>
> toomany:
> echo " too many processors for this test, exiting (Max = 2)"
> echo "============================================================"
> exit(0)
>

I then commented the line you told me by adding a # in front of it

This is what I did in the terminal then:

> kunin_at_admin-laptop:~/amber10/test/tgtmd/change_target.ntr$ ./Run.tgtmd
> SANDER: Targeted MD with changing target and restraints
> diffing tgtmd.out.save with tgtmd.out
> PASSED
> ==============================================================
> kunin_at_admin-laptop:~/amber10/test/tgtmd/change_target.ntr$
>

This is tgtmd.out, which the second time I did this actually had stuff in
it.

> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | Run on 11/17/2009 at 10:16:45
> [-O]verwriting output
>
> File Assignments:
> | MDIN: tgtmd.in
>
> | MDOUT:
> tgtmd.out
> |INPCRD:
> inpcrd
> | PARM:
> prmtop
> |RESTRT:
> tgtmd.restrt
> | REFC:
> refcrd
> | MDVEL:
> mdvel
> | MDEN:
> mden
> | MDCRD:
> tgtmd.trj
> |MDINFO: tgtmd.info
>
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
> |INPTRA:
> inptraj
> |
>
> Here is the input file:
>
> inpcrd->refcrd tgtmd: regular vacuum md, backbone
> restrained
> &cntrl
>
> imin = 0, ntx = 1, nstlim =
> 1000,
> dt = 0.002, ntc = 2, ntf = 2, tol =
> 0.000001,
> tempi = 300.0, temp0 =
> 300.0,
> scee = 1.2, cut =
> 10.0,
> ntpr = 50, ntwx = 50, ntwr =
> 500,
> ntb = 0, ntt = 1, tautp = 0.5, ntp =
> 0,
> igb = 0, nscm = 0, nmropt = 1, ntr =
> 1,
> restraintmask="@CA,C,O,N,H,HA",
> restraint_wt=5.0,
> itgtmd = 1, tgtrmsd = 5.516, tgtmdfrc =
> 2.0,
> tgtrmsmask=":TYR &
> !@CA,C,O,N,H,HA",
> /
>
> &ewald
>
> use_pme = 0, vdwmeth = 0, eedmeth =
> 4,
> /
>
> &wt
>
> TYPE='TGTRMSD', istep1=1,
> istep2=1000,
> value1 = 5.516, value2 =
> 0.0,
> /
>
> &wt
>
>
> type="END",
> /
>
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> |
> Flags:
>
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> | *** cutoff > system size, list only builds once
> |Largest sphere to fit in unit cell has radius = 33.789
> | New format PARM file being parsed.
> | Version = 1.000 Date = 01/08/04 Time = 16:06:48
> NATOM = 44 NTYPES = 11 NBONH = 21 MBONA = 23
> NTHETH = 45 MTHETA = 31 NPHIH = 80 MPHIA = 47
> NHPARM = 0 NPARM = 0 NNB = 225 NRES = 3
> NBONA = 23 NTHETA = 31 NPHIA = 47 NUMBND = 18
> NUMANG = 33 NPTRA = 18 NATYP = 14 NPHB = 0
> IFBOX = 0 NMXRS = 22 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 3672
> | Hollerith 269
> | Integer 23793
> | Max Pairs 946
> | nblistReal 528
> | nblist Int 441796
> | Total 1856 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
>
> --------------------------------------------------------------------------------
> 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 = 50, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 50, ntwv = 0, ntwe
> = 0
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 2, ntb = 0, igb = 0, nsnb
> = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Molecular dynamics:
> nstlim = 1000, nscm = 999999999, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>
> Berendsen (weak-coupling) temperature regulation:
> temp0 = 300.00000, tempi = 300.00000, tautp = 0.50000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00000
>
> NMR refinement options:
> iscale = 0, noeskp = 1, ipnlty = 1, mxsub
> = 1
> scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>
> Targeted molecular dynamics:
> tgtrmsd = 5.51600, tgtmdfrc= 2.00000
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> LOADING THE TARGETED MD ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> | INFO: Old style inpcrd file read
>
> Mask @CA,C,O,N,H,HA; matches 17 atoms
> Mask ":TYR & !@CA,C,O,N,H,HA" matches 16 atoms
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
>
>
> begin time read from input coords = 0.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TGTRMSD 1 1000 5.516000 0.000000 0 0
>
> RESTRAINTS:
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = -0.00000000
> Forcing neutrality...
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 111.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 111. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 111.
> | TOTAL # of degrees of freedom (RNDF) = 111.
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 723
> | TOTAL SIZE OF NONBOND LIST = 723
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 352.21 PRESS =
> 0.0
> Etot = 71.9151 EKtot = 38.8450 EPtot =
> 33.0701
> BOND = 0.8576 ANGLE = 4.6686 DIHED =
> 8.2100
> 1-4 NB = 16.1547 1-4 EEL = 214.7840 VDWAALS =
> 52.7343
> EELEC = -264.3393 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EAMBER (non-restraint) = 33.0701
> Current RMSD from reference: 5.516
> Current target RMSD: 5.516
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 420.47 PRESS =
> 0.0
> Etot = 71.4948 EKtot = 46.3733 EPtot =
> 25.1215
> BOND = 6.2383 ANGLE = 23.8280 DIHED =
> 14.1073
> 1-4 NB = 14.6361 1-4 EEL = 215.6117 VDWAALS =
> -4.1017
> EELEC = -266.1244 EHBOND = 0.0000 RESTRAINT =
> 20.9263
> EAMBER (non-restraint) = 4.1952
> Current RMSD from reference: 5.825
> Current target RMSD: 5.251
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 453.35 PRESS =
> 0.0
> Etot = 76.2450 EKtot = 49.9995 EPtot =
> 26.2455
> BOND = 7.3045 ANGLE = 35.0076 DIHED =
> 12.7055
> 1-4 NB = 9.6081 1-4 EEL = 218.5458 VDWAALS =
> -1.6726
> EELEC = -267.5168 EHBOND = 0.0000 RESTRAINT =
> 12.2633
> EAMBER (non-restraint) = 13.9822
> Current RMSD from reference: 5.639
> Current target RMSD: 4.975
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 482.49 PRESS =
> 0.0
> Etot = 79.3485 EKtot = 53.2130 EPtot =
> 26.1355
> BOND = 8.3076 ANGLE = 27.9135 DIHED =
> 13.2098
> 1-4 NB = 18.2073 1-4 EEL = 219.3339 VDWAALS =
> -4.7004
> EELEC = -267.2737 EHBOND = 0.0000 RESTRAINT =
> 11.1374
> EAMBER (non-restraint) = 14.9981
> Current RMSD from reference: 4.952
> Current target RMSD: 4.699
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 527.42 PRESS =
> 0.0
> Etot = 55.8715 EKtot = 58.1689 EPtot =
> -2.2974
> BOND = 10.7101 ANGLE = 14.3521 DIHED =
> 15.9101
> 1-4 NB = 15.4296 1-4 EEL = 215.1856 VDWAALS =
> -2.8969
> EELEC = -277.7582 EHBOND = 0.0000 RESTRAINT =
> 6.7701
> EAMBER (non-restraint) = -9.0675
> Current RMSD from reference: 4.177
> Current target RMSD: 4.423
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 250 TIME(PS) = 0.500 TEMP(K) = 421.77 PRESS =
> 0.0
> Etot = 72.8020 EKtot = 46.5170 EPtot =
> 26.2850
> BOND = 8.7619 ANGLE = 20.3698 DIHED =
> 14.2863
> 1-4 NB = 11.0133 1-4 EEL = 210.7450 VDWAALS =
> -4.4584
> EELEC = -245.6034 EHBOND = 0.0000 RESTRAINT =
> 11.1705
> EAMBER (non-restraint) = 15.1145
> Current RMSD from reference: 3.693
> Current target RMSD: 4.147
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = 335.99 PRESS =
> 0.0
> Etot = 51.4071 EKtot = 37.0562 EPtot =
> 14.3509
> BOND = 10.0135 ANGLE = 25.5682 DIHED =
> 16.6515
> 1-4 NB = 11.0866 1-4 EEL = 216.0508 VDWAALS =
> -4.1023
> EELEC = -269.6235 EHBOND = 0.0000 RESTRAINT =
> 8.7060
> EAMBER (non-restraint) = 5.6449
> Current RMSD from reference: 3.739
> Current target RMSD: 3.871
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 350 TIME(PS) = 0.700 TEMP(K) = 336.30 PRESS =
> 0.0
> Etot = 57.2583 EKtot = 37.0897 EPtot =
> 20.1686
> BOND = 6.4142 ANGLE = 29.9483 DIHED =
> 18.5351
> 1-4 NB = 11.7390 1-4 EEL = 207.5498 VDWAALS =
> -4.4903
> EELEC = -257.4666 EHBOND = 0.0000 RESTRAINT =
> 7.9392
> EAMBER (non-restraint) = 12.2294
> Current RMSD from reference: 3.961
> Current target RMSD: 3.595
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 323.55 PRESS =
> 0.0
> Etot = 48.3759 EKtot = 35.6837 EPtot =
> 12.6922
> BOND = 7.8776 ANGLE = 23.8808 DIHED =
> 18.4025
> 1-4 NB = 16.5332 1-4 EEL = 221.3869 VDWAALS =
> -2.7669
> EELEC = -287.2586 EHBOND = 0.0000 RESTRAINT =
> 14.6368
> EAMBER (non-restraint) = -1.9446
> Current RMSD from reference: 3.850
> Current target RMSD: 3.318
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 450 TIME(PS) = 0.900 TEMP(K) = 324.33 PRESS =
> 0.0
> Etot = 61.1667 EKtot = 35.7703 EPtot =
> 25.3964
> BOND = 7.4976 ANGLE = 27.5892 DIHED =
> 19.7958
> 1-4 NB = 15.9782 1-4 EEL = 212.1934 VDWAALS =
> -3.6822
> EELEC = -266.9554 EHBOND = 0.0000 RESTRAINT =
> 12.9798
> EAMBER (non-restraint) = 12.4165
> Current RMSD from reference: 3.453
> Current target RMSD: 3.042
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 421.40 PRESS =
> 0.0
> Etot = 62.2513 EKtot = 46.4762 EPtot =
> 15.7751
> BOND = 8.7591 ANGLE = 20.2529 DIHED =
> 15.5157
> 1-4 NB = 13.6066 1-4 EEL = 213.1424 VDWAALS =
> -3.6638
> EELEC = -264.4624 EHBOND = 0.0000 RESTRAINT =
> 12.6245
> EAMBER (non-restraint) = 3.1506
> Current RMSD from reference: 2.946
> Current target RMSD: 2.766
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 550 TIME(PS) = 1.100 TEMP(K) = 381.22 PRESS =
> 0.0
> Etot = 68.3194 EKtot = 42.0444 EPtot =
> 26.2750
> BOND = 8.6402 ANGLE = 29.8254 DIHED =
> 15.4021
> 1-4 NB = 12.5348 1-4 EEL = 210.0746 VDWAALS =
> -2.1935
> EELEC = -258.7799 EHBOND = 0.0000 RESTRAINT =
> 10.7714
> EAMBER (non-restraint) = 15.5036
> Current RMSD from reference: 2.566
> Current target RMSD: 2.490
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 600 TIME(PS) = 1.200 TEMP(K) = 376.31 PRESS =
> 0.0
> Etot = 57.0500 EKtot = 41.5026 EPtot =
> 15.5474
> BOND = 7.5570 ANGLE = 26.8981 DIHED =
> 20.0671
> 1-4 NB = 11.4978 1-4 EEL = 208.5961 VDWAALS =
> -3.7700
> EELEC = -264.3832 EHBOND = 0.0000 RESTRAINT =
> 9.0846
> EAMBER (non-restraint) = 6.4629
> Current RMSD from reference: 2.415
> Current target RMSD: 2.214
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 650 TIME(PS) = 1.300 TEMP(K) = 413.20 PRESS =
> 0.0
> Etot = 61.6817 EKtot = 45.5713 EPtot =
> 16.1104
> BOND = 7.5926 ANGLE = 21.9704 DIHED =
> 16.9573
> 1-4 NB = 15.1143 1-4 EEL = 218.6652 VDWAALS =
> -1.0314
> EELEC = -273.1592 EHBOND = 0.0000 RESTRAINT =
> 10.0013
> EAMBER (non-restraint) = 6.1091
> Current RMSD from reference: 2.149
> Current target RMSD: 1.938
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 700 TIME(PS) = 1.400 TEMP(K) = 521.86 PRESS =
> 0.0
> Etot = 67.7665 EKtot = 57.5554 EPtot =
> 10.2111
> BOND = 7.4772 ANGLE = 17.7041 DIHED =
> 10.2265
> 1-4 NB = 15.4663 1-4 EEL = 222.0191 VDWAALS =
> -2.8236
> EELEC = -264.8669 EHBOND = 0.0000 RESTRAINT =
> 5.0085
> EAMBER (non-restraint) = 5.2026
> Current RMSD from reference: 1.678
> Current target RMSD: 1.662
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 750 TIME(PS) = 1.500 TEMP(K) = 432.57 PRESS =
> 0.0
> Etot = 71.2230 EKtot = 47.7076 EPtot =
> 23.5154
> BOND = 9.1809 ANGLE = 16.5640 DIHED =
> 12.5317
> 1-4 NB = 10.3204 1-4 EEL = 208.7359 VDWAALS =
> -5.0096
> EELEC = -238.2734 EHBOND = 0.0000 RESTRAINT =
> 9.4655
> EAMBER (non-restraint) = 14.0499
> Current RMSD from reference: 1.431
> Current target RMSD: 1.386
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 800 TIME(PS) = 1.600 TEMP(K) = 420.72 PRESS =
> 0.0
> Etot = 58.9942 EKtot = 46.4007 EPtot =
> 12.5935
> BOND = 7.2057 ANGLE = 14.5308 DIHED =
> 16.4516
> 1-4 NB = 10.7504 1-4 EEL = 215.9988 VDWAALS =
> -3.5620
> EELEC = -257.8618 EHBOND = 0.0000 RESTRAINT =
> 9.0800
> EAMBER (non-restraint) = 3.5134
> Current RMSD from reference: 1.444
> Current target RMSD: 1.110
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 850 TIME(PS) = 1.700 TEMP(K) = 399.00 PRESS =
> 0.0
> Etot = 58.3068 EKtot = 44.0053 EPtot =
> 14.3015
> BOND = 8.8448 ANGLE = 16.5235 DIHED =
> 15.2614
> 1-4 NB = 11.6528 1-4 EEL = 216.9395 VDWAALS =
> -2.3895
> EELEC = -262.1591 EHBOND = 0.0000 RESTRAINT =
> 9.6281
> EAMBER (non-restraint) = 4.6733
> Current RMSD from reference: 1.318
> Current target RMSD: 0.834
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 900 TIME(PS) = 1.800 TEMP(K) = 466.93 PRESS =
> 0.0
> Etot = 60.7107 EKtot = 51.4979 EPtot =
> 9.2128
> BOND = 7.3891 ANGLE = 14.0386 DIHED =
> 15.9439
> 1-4 NB = 10.0327 1-4 EEL = 215.6217 VDWAALS =
> -4.1054
> EELEC = -257.9509 EHBOND = 0.0000 RESTRAINT =
> 8.2431
> EAMBER (non-restraint) = 0.9697
> Current RMSD from reference: 0.907
> Current target RMSD: 0.558
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 950 TIME(PS) = 1.900 TEMP(K) = 389.17 PRESS =
> 0.0
> Etot = 65.1975 EKtot = 42.9211 EPtot =
> 22.2763
> BOND = 6.6787 ANGLE = 17.6618 DIHED =
> 14.1099
> 1-4 NB = 9.8918 1-4 EEL = 210.9029 VDWAALS =
> -4.2304
> EELEC = -247.9439 EHBOND = 0.0000 RESTRAINT =
> 15.2055
> EAMBER (non-restraint) = 7.0708
> Current RMSD from reference: 0.966
> Current target RMSD: 0.282
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 376.63 PRESS =
> 0.0
> Etot = 62.5577 EKtot = 41.5381 EPtot =
> 21.0195
> BOND = 6.5204 ANGLE = 18.3486 DIHED =
> 13.7704
> 1-4 NB = 11.2716 1-4 EEL = 216.2527 VDWAALS =
> -2.4448
> EELEC = -265.8082 EHBOND = 0.0000 RESTRAINT =
> 23.1089
> EAMBER (non-restraint) = -2.0894
> Current RMSD from reference: 0.990
> Current target RMSD: 0.006
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> A V E R A G E S O V E R 1000 S T E P S
>
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 417.36 PRESS =
> 0.0
> Etot = 64.4205 EKtot = 46.0300 EPtot =
> 18.3905
> BOND = 8.3352 ANGLE = 21.6557 DIHED =
> 15.1591
> 1-4 NB = 12.5151 1-4 EEL = 213.5146 VDWAALS =
> -3.1914
> EELEC = -260.2705 EHBOND = 0.0000 RESTRAINT =
> 10.6727
> EAMBER (non-restraint) = 7.7177
> Current RMSD from reference: 0.990
> Current target RMSD: 0.006
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 61.38 PRESS =
> 0.0
> Etot = 7.6008 EKtot = 6.7695 EPtot =
> 8.1078
> BOND = 2.5729 ANGLE = 4.6774 DIHED =
> 2.8467
> 1-4 NB = 2.2154 1-4 EEL = 3.8020 VDWAALS =
> 2.9921
> EELEC = 9.0931 EHBOND = 0.0000 RESTRAINT =
> 4.0138
> EAMBER (non-restraint) = 4.0940
> Current RMSD from reference: 0.990
> Current target RMSD: 0.006
>
> ------------------------------------------------------------------------------
>
>
> NMR restraints on final step:
>
>
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
>
> --------------------------------------------------------------------------------
>
> | Read coords time 0.00 ( 0.28% of Total)
> | Fast Water setup 0.00 ( 0.01% of Total)
> | Build the list 0.01 (84.98% of List )
> | Other 0.00 (15.02% of List )
> | List time 0.01 ( 9.38% of Nonbo)
> | Short_ene time 0.06 (94.41% of Direc)
> | Other 0.00 ( 5.59% of Direc)
> | Direct Ewald time 0.07 (80.09% of Ewald)
> | Force Adjust 0.00 ( 2.28% of Ewald)
> | Virial junk 0.00 ( 1.71% of Ewald)
> | Start sycnronization 0.00 ( 1.75% of Ewald)
> | Other 0.01 (14.18% of Ewald)
> | Ewald time 0.09 (82.94% of Nonbo)
> | IPS excludes 0.00 ( 1.26% of Nonbo)
> | Other 0.01 ( 6.41% of Nonbo)
> | Nonbond force 0.10 (51.75% of Force)
> | Bond/Angle/Dihedral 0.08 (40.79% of Force)
> | Other 0.01 ( 7.47% of Force)
> | Force time 0.20 (80.49% of Runmd)
> | Shake time 0.01 ( 2.39% of Runmd)
> | Verlet update time 0.02 ( 6.11% of Runmd)
> | Other 0.03 (11.01% of Runmd)
> | Runmd Time 0.25 (81.60% of Total)
> | Other 0.05 (18.11% of Total)
> | Total time 0.30 (96.30% of ALL )
>
> | Highest rstack allocated: 175
> | Highest istack allocated: 35
> | Job began at 10:16:45.867 on 11/17/2009
> | Setup done at 10:16:45.941 on 11/17/2009
> | Run done at 10:16:46.189 on 11/17/2009
> | wallclock() was called 29035 times
>

Hopefully that clarifies things.
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