Custom Search
--
********************************
Grzegorz Jezierski
Biophysics Department
Institute of Molecular Biology
Jagiellonian University
al. Mickiewicza 3, 31-120 Krakow
ph.:(48 12)6341305 ext.291
e-mail: gj_at_mol.uj.edu.pl
********************************
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Sat Dec 9 15:51:15 2000
[-O]verwriting output
File Assignments:
|MDIN : /disk2/usr/people/ubjezier/tmp/dyn0_api_dimer_wat.inp
|MDOUT: /disk2/usr/people/ubjezier/tmp/dyn1_api_dimer_wat.out
|INPCR: /disk2/usr/people/ubjezier/SANDER/DIMER/RST/minm_api_dimer_wat.crd
|PARM : /disk2/usr/people/ubjezier/SANDER/DIMER/minm_api_dimer_wat.top
|RESTR: /disk2/usr/people/ubjezier/tmp/dyn0_api_dimer_wat.rst
|REFC : refc
|MDVEL: /scratch/ubjezier/SANDER/DIMER/dyn0_api_dimer_wat.vel
|MDEN : /scratch/ubjezier/SANDER/DIMER/dyn0_api_dimer_wat.ene
|MDCRD: /scratch/ubjezier/SANDER/DIMER/dyn0_api_dimer_wat.xyz
|MDINF: mdinfo
Here is the input file:
# AMBER6 - Sander
# test
#
&cntrl
timlim=999999., imin=0, nmropt=1,
ntx=1, irest=0,
ntwx=50, ntwv=50, ntwe=50,
ntf=2, ntb=2,
cut=12., nsnb=20, scnb=2.0, scee=1.2,
dt=0.002, nstlim=10000,
ndfmin=6, ntcm=1,
ntt=1, tautp=0.4, vlimit=10.,
ntc=2, tol=0.0005,
ntp=1,
&end
&ewald
a=86., b=99., c=101.,
alpha=90., beta=90., gamma=90.,
nfft1=90, nfft2=100, nfft3=100,
order=5, ischrgd=0, verbose=3, ew_type=0,
opt_infl=1,
&end
# 10.0 K --> 310 K
#
#
#
&wt type='TEMP0', istep1= 1, istep2=10000,
value1= 10.0, value2= 305.0, &end
#
&wt type='END' &end
#
-------------------------------------------------------------------------------
# AMBER6 - Sander
1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
EWALD SPECIFIC INPUT:
| Using the SGI specific (ZFFT3D) Fast Fourier Transform
Largest sphere to fit in unit cell has radius = 43.000
Calculating ew_coeff from dsum_tol,cutoff
Box X = 86.000 Box Y = 99.000 Box Z = 101.000
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 90 NFFT2 = 100 NFFT3 = 100
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 5
NATOM = 77998 NTYPES = 16 NBONH = 72038 MBONA = 6086
NTHETH = 13804 MTHETA = 8226 NPHIH = 24722 MPHIA = 14500
NHPARM = 0 NPARM = 0 NNB = 154598 NRES = 22752
NBONA = 6086 NTHETA = 8226 NPHIA = 14500 NUMBND = 44
NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0
EWALD MEMORY USE:
| Total heap storage needed = 976
| Adjacent nonbond minimum mask = 154598
| Max number of pointers = 25
| List build maxmask = 309196
Number of grids per unit cell in each dimension:
19 22 23
Unit cell edge lengths in each dimension:
86.000 99.000 101.000
Distance between parallel faces of unit cell:
86.000 99.000 101.000
Distance between faces of short range grid subcells:
4.526 4.500 4.391
Resulting cutoff from subcell neighborhoods is 13.174
| Maximage = 114120
EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 976
| Size of EEDTABLE = 20397
| Real memory needed by EEDTABLE = 81588
| Integer memory needed by ADJ = 309196
| Integer memory used by local nonb= 2358346
| Real memory used by local nonb = 1278336
| MAX NONBOND PAIRS = 40000000
| Memory Use Allocated Used
| Real 4500000 4403612
| Hollerith 500000 490742
| Integer 4500000 4246637
| Max Nonbonded Pairs:40000000
BOX TYPE: RECTILINEAR
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
IMIN = 0
IPOL = 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 2 BOXX = 86.000
BOXY = 99.000 BOXZ = 101.000
NTT = 1 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.400
VLIMIT= 10.000
NTP = 1 PRES0 = 1.000 COMP = 44.600
TAUP = 0.200 NPSCAL= 0
NTCM = 1 NSCM = 9999999
NSTLIM=10000 NTU = 1
T = 0.000 DT = 0.00200
NTC = 2 TOL = 0.00050 JFASTW = 0
NTF = 2 NSNB = 20
CUT = 12.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
NTPR = 50 NTWR = 50 NTWX = 50
NTWV = 50 NTWE = 50 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0 NTAVE= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
VRAND= 0
NATOM = 77998 NRES = 22752
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
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 1 10000 10.000000 305.000000 0 0
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 22002
Sum of charges from parm topology file = 3.99999966
Forcing neutrality...
---------------------------------------------------
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 = 0.2088E-14 at 2.598900
| CHECK d/dx switch(x): max rel err = 0.7404E-11 at 2.716040
---------------------------------------------------
Total number of mask terms = 131962
Total number of mask terms = 263924
| Total Ewald setup time = 0.28641510
------------------------------------------------------------------------------
Number of grids per unit cell in each dimension:
19 22 23
Unit cell edge lengths in each dimension:
86.000 99.000 101.000
Distance between parallel faces of unit cell:
86.000 99.000 101.000
Distance between faces of short range grid subcells:
4.526 4.500 4.391
Resulting cutoff from subcell neighborhoods is 13.174
listtot = 32545676
NET FORCE PER ATOM: 0.1745E-06 0.1165E-05 -0.3693E-06
Evdw = 249622.275828485520
Ehbond = 0.000000000000
Ecoulomb = -279004.847800189980
E polarization = 0.000000000000
Iso virial = ********************
Eevir vs. Ecoulomb = 0.000226418806
E electrostatic (self) = ********************
(rec) = 2948.078622037556
(dir) = -232908.713641980690
(adj) = 982012.345154466220
MOLECULAR VIRIAL: -.15991891E+07 -.84128658E+06 -.79115253E+06
MOLECULAR VIRIAL: -.87885154E+06 -.65542372E+06 -.45359789E+06
MOLECULAR VIRIAL: -.86684555E+06 -.47966465E+06 -.46652715E+06
--------------------------------------------
Reciprocal VIRIAL: 0.10458615E+04 0.43218637E+02 0.15243193E+02
Reciprocal VIRIAL: 0.43218637E+02 0.92502470E+03 -.14737839E+02
Reciprocal VIRIAL: 0.15243193E+02 -.14737839E+02 0.10064738E+04
..................
Direct VIRIAL: -.17123143E+07 -.82312606E+06 -.82920293E+06
Direct VIRIAL: -.82312606E+06 -.85195194E+06 -.47910345E+06
Direct VIRIAL: -.82920293E+06 -.47910345E+06 -.67339549E+06
..................
Dir Sum EE vir trace: 0.28152711E+06
..................
Adjust VIRIAL: -.19827198E+04 0.38186547E+03 0.10133467E+03
Adjust VIRIAL: 0.38186547E+03 -.18813770E+04 -.20141948E+03
Adjust VIRIAL: 0.10133467E+03 -.20141948E+03 -.16986997E+04
..................
Recip Disp. VIRIAL: 0.14223011E+04 0.00000000E+00 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.14223011E+04 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.00000000E+00 0.14223011E+04
..................
Self VIRIAL: 0.59405747E-25 0.00000000E+00 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.59405747E-25 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.00000000E+00 0.59405747E-25
..................
Atomic VIRIAL: -.17118289E+07 -.82270098E+06 -.82908636E+06
Atomic VIRIAL: -.82270098E+06 -.85148599E+06 -.47931961E+06
Atomic VIRIAL: -.82908636E+06 -.47931961E+06 -.67266541E+06
--------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 73280.43
Etot = 20918.7617 EKtot = 0.0000 EPtot = 20918.7617
BOND = 112.9273 ANGLE = 1986.6669 DIHED = 3968.4008
1-4 NB = 3815.9359 1-4 EEL = 40417.4028 VDWAALS = 249622.2758
EELEC = -279004.8478 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = ************ VOLUME = 859914.0000
Density = 0.9286
Ewald error estimate: 0.2264E-03
------------------------------------------------------------------------------
===============================================================================
(...)
--------------------------------------------
NET FORCE PER ATOM: -0.4179E-08 0.1186E-06 -0.8845E-08
Evdw = 24398.357846871088
Ehbond = 0.000000000000
Ecoulomb = -311493.139739089650
E polarization = 0.000000000000
Iso virial = 38923.537173065808
Eevir vs. Ecoulomb = 0.000028706460
E electrostatic (self) = ********************
(rec) = 667.214256473720
(dir) = -263481.109116094830
(adj) = 982377.313055244510
MOLECULAR VIRIAL: 0.15747770E+05 0.17181862E+04 -.64926791E+03
MOLECULAR VIRIAL: 0.45996152E+03 0.99149857E+04 0.64887376E+03
MOLECULAR VIRIAL: -.54430429E+03 0.16313089E+04 0.13260782E+05
--------------------------------------------
Reciprocal VIRIAL: 0.45272556E+03 0.42370899E+01 0.95089479E+01
Reciprocal VIRIAL: 0.42370899E+01 0.45829689E+03 0.27455895E+02
Reciprocal VIRIAL: 0.95089479E+01 0.27455895E+02 0.43434164E+03
..................
Direct VIRIAL: -.18164333E+06 0.35636644E+02 0.47435828E+03
Direct VIRIAL: 0.35636644E+02 -.18449087E+06 -.95989153E+03
Direct VIRIAL: 0.47435828E+03 -.95989153E+03 -.18368996E+06
..................
Dir Sum EE vir trace: 0.31521993E+06
..................
Adjust VIRIAL: -.15898210E+04 0.92376608E-01 -.55786866E+01
Adjust VIRIAL: 0.92376608E-01 -.19355756E+04 -.34722539E+03
Adjust VIRIAL: -.55786866E+01 -.34722539E+03 -.15556972E+04
..................
Recip Disp. VIRIAL: 0.15787561E+04 0.00000000E+00 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.15787561E+04 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.00000000E+00 0.15787561E+04
..................
Self VIRIAL: 0.65940459E-25 0.00000000E+00 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.65940459E-25 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.00000000E+00 0.65940459E-25
..................
Atomic VIRIAL: -.18120167E+06 0.39966110E+02 0.47828854E+03
Atomic VIRIAL: 0.39966110E+02 -.18438940E+06 -.12796610E+04
Atomic VIRIAL: 0.47828854E+03 -.12796610E+04 -.18323256E+06
--------------------------------------------
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 287.47 PRESS = -8.44
Etot = -188248.6089 EKtot = 46259.1091 EPtot = -234507.7180
BOND = 1695.5459 ANGLE = 5287.5941 DIHED = 4794.2389
1-4 NB = 2724.7992 1-4 EEL = 38084.8859 VDWAALS = 24398.3578
EELEC = -311493.1397 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 19320.6430 VIRIAL = 19461.7686 VOLUME = 774696.3573
Density = 1.0308
Ewald error estimate: 0.2871E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 10000
Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
A V E R A G E S O V E R 10000 S T E P S
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 170.23 PRESS = -22.24
Etot = -236033.1404 EKtot = 27392.5047 EPtot = -263425.6451
BOND = 850.9281 ANGLE = 3157.0757 DIHED = 4321.7240
1-4 NB = 2571.2036 1-4 EEL = 38244.9493 VDWAALS = 35844.1576
EELEC = -348415.6834 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 12783.8401 VIRIAL = 13179.4203 VOLUME = 786509.2014
Density = 1.0185
Ewald error estimate: 0.6685E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 10000
Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
R M S F L U C T U A T I O N S
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 84.57 PRESS = 866.68
Etot = 30772.4516 EKtot = 13608.1065 EPtot = 17955.8499
BOND = 379.4596 ANGLE = 931.8914 DIHED = 218.7334
1-4 NB = 65.8161 1-4 EEL = 75.9793 VDWAALS = 6442.9163
EELEC = 22474.1805 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 8010.3208 VIRIAL = 15321.4821 VOLUME = 48192.5522
Density = 0.0525
Ewald error estimate: 0.5561E-04
------------------------------------------------------------------------------
NMR restraints on final step:
|
| ELAPSED TIME = 294745.706 TOTAL TIME = 294745.706
|
Nonbond Ewald pairlist time components:
| map, save_t = 270.16 0.09
| grid setup_t = 0.00 0.00
| grid ucell_t = 59.92 0.02
| grid image_t = 127.35 0.04
| build list_t = 31449.68 10.67
| total list_t = 31907.11 10.83
Nonbond Ewald force time components:
| zero ene,force = 184.13 0.06
| map = 0.00 0.00
| map,adjust = 1677.46 0.57
| self energy = 0.20 0.00
| 1-dim b-spline= 5131.35 1.74
| grid charges = 15749.14 5.34
| scalar sum = 8206.77 2.78
| grad sum = 19628.39 6.66
| FFT = 16941.23 5.75
| Recip force = 65656.89 22.28
| Direct force = 183124.89 62.13
| adjust masked = 1245.00 0.42
| accum force = 0.39 0.00
| finish virial = 890.89 0.30
| mfct4 = 0.20 0.00
| f_wait = 0.25 0.00
| stack_time = 0.77 0.00
| total force = 252781.05 85.76
|
| Routine Sec %
| ----------------------------
| Nonbond 285140.60 96.74
| Bond 131.19 0.04
| Angle 667.18 0.23
| Dihedral 3240.40 1.10
| Shake 1013.86 0.34
| GBrad 0.00 0.00
| Force 0.00 0.00
| Other 4552.49 1.54
| ----------------------------
| Total 294745.71 81.87 Hours
| Nonsetup 294630.81 99.96%
| Highest rstack allocated: 4430516
| MAX_RSTACK = 5000000
| Highest istack allocated: 77998
| MAX_ISTACK = 100000
| Setup wallclock 134 seconds
| Nonsetup wallclock 331257 seconds
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Mon Dec 18 15:03:10 2000
[-O]verwriting output
File Assignments:
|MDIN : /disk2/usr/people/ubjezier/tmp/dyn1_api_dimer_wat.inp
|MDOUT: /disk2/usr/people/ubjezier/tmp/dyn1_api_dimer_wat.out
|INPCR: /disk2/usr/people/ubjezier/SANDER/DIMER/RST/dyn0_api_dimer_wat.rst
|PARM : /disk2/usr/people/ubjezier/SANDER/DIMER/minm_api_dimer_wat.top
|RESTR: /disk2/usr/people/ubjezier/SANDER/DIMER/RST/dyn1_api_dimer_wat.rst
|REFC : refc
|MDVEL: /scratch/ubjezier/SANDER/DIMER/dyn1_api_dimer_wat.vel
|MDEN : /scratch/ubjezier/SANDER/DIMER/dyn1_api_dimer_wat.ene
|MDCRD: /scratch/ubjezier/SANDER/DIMER/dyn1_api_dimer_wat.xyz
|MDINF: mdinfo
Here is the input file:
# AMBER6 - Sander
# test
#
&cntrl
timlim=999999., imin=0, nmropt=1,
ntx=1, irest=0,
ntwx=50, ntwv=50, ntwe=50,
ntf=2, ntb=2,
cut=12., nsnb=20, scnb=2.0, scee=1.2,
dt=0.002, nstlim=10000,
ndfmin=6, ntcm=1,
ntt=1, tautp=0.4, vlimit=10.,
ntc=2, tol=0.0005,
ntp=1, pres0=1.0, comp=44.6, taup=0.6,
&end
&ewald
a=86., b=99., c=101.,
alpha=90., beta=90., gamma=90.,
nfft1=90, nfft2=100, nfft3=100,
order=5, ischrgd=0, verbose=3, ew_type=0,
opt_infl=1,
&end
# 310 K
#
#
#
&wt type='TEMP0', istep1= 1, istep2=10000,
value1= 305.0, value2= 315.0, &end
#
&wt type='END' &end
#
-------------------------------------------------------------------------------
# AMBER6 - Sander
1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
EWALD SPECIFIC INPUT:
| Using the SGI specific (ZFFT3D) Fast Fourier Transform
Largest sphere to fit in unit cell has radius = 43.000
Calculating ew_coeff from dsum_tol,cutoff
Box X = 86.000 Box Y = 99.000 Box Z = 101.000
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 90 NFFT2 = 100 NFFT3 = 100
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 5
NATOM = 77998 NTYPES = 16 NBONH = 72038 MBONA = 6086
NTHETH = 13804 MTHETA = 8226 NPHIH = 24722 MPHIA = 14500
NHPARM = 0 NPARM = 0 NNB = 154598 NRES = 22752
NBONA = 6086 NTHETA = 8226 NPHIA = 14500 NUMBND = 44
NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0
EWALD MEMORY USE:
| Total heap storage needed = 976
| Adjacent nonbond minimum mask = 154598
| Max number of pointers = 25
| List build maxmask = 309196
Number of grids per unit cell in each dimension:
19 22 23
Unit cell edge lengths in each dimension:
86.000 99.000 101.000
Distance between parallel faces of unit cell:
86.000 99.000 101.000
Distance between faces of short range grid subcells:
4.526 4.500 4.391
Resulting cutoff from subcell neighborhoods is 13.174
| Maximage = 114120
EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 976
| Size of EEDTABLE = 20397
| Real memory needed by EEDTABLE = 81588
| Integer memory needed by ADJ = 309196
| Integer memory used by local nonb= 2358346
| Real memory used by local nonb = 1278336
| MAX NONBOND PAIRS = 40000000
| Memory Use Allocated Used
| Real 4500000 4403612
| Hollerith 500000 490742
| Integer 4500000 4246637
| Max Nonbonded Pairs:40000000
BOX TYPE: RECTILINEAR
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
IMIN = 0
IPOL = 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 2 BOXX = 86.000
BOXY = 99.000 BOXZ = 101.000
NTT = 1 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.400
VLIMIT= 10.000
NTP = 1 PRES0 = 1.000 COMP = 44.600
TAUP = 0.600 NPSCAL= 0
NTCM = 1 NSCM = 9999999
NSTLIM=10000 NTU = 1
T = 0.000 DT = 0.00200
NTC = 2 TOL = 0.00050 JFASTW = 0
NTF = 2 NSNB = 20
CUT = 12.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
NTPR = 50 NTWR = 50 NTWX = 50
NTWV = 50 NTWE = 50 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0 NTAVE= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
VRAND= 0
NATOM = 77998 NRES = 22752
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
3. ATOMIC COORDINATES AND VELOCITIES
begin time read from input coords = 20.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 1 10000 305.000000 315.000000 0 0
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 22002
Sum of charges from parm topology file = 3.99999966
Forcing neutrality...
---------------------------------------------------
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 = 0.2088E-14 at 2.598900
| CHECK d/dx switch(x): max rel err = 0.7404E-11 at 2.716040
---------------------------------------------------
Total number of mask terms = 131962
Total number of mask terms = 263924
| Total Ewald setup time = 0.39832306
------------------------------------------------------------------------------
Number of grids per unit cell in each dimension:
19 22 23
Unit cell edge lengths in each dimension:
86.000 99.000 101.000
Distance between parallel faces of unit cell:
86.000 99.000 101.000
Distance between faces of short range grid subcells:
4.526 4.500 4.391
Resulting cutoff from subcell neighborhoods is 13.174
listtot = 32954236
NET FORCE PER ATOM: 0.1557E-07 0.1994E-06 0.3748E-07
Evdw = ********************
Ehbond = 0.000000000000
Ecoulomb = -284831.768854982570
E polarization = 0.000000000000
Iso virial = ********************
Eevir vs. Ecoulomb = 0.000033574475
E electrostatic (self) = ********************
(rec) = 1158.665097299469
(dir) = -237313.604831216890
(adj) = 982379.728813647870
MOLECULAR VIRIAL: -.40483186E+13 -.43024895E+13 0.18530676E+13
MOLECULAR VIRIAL: -.51988030E+13 -.84055000E+13 0.45371267E+13
MOLECULAR VIRIAL: 0.19878506E+13 0.54599166E+13 -.35002724E+13
--------------------------------------------
Reciprocal VIRIAL: 0.91947519E+03 -.22768708E+02 0.12595893E+02
Reciprocal VIRIAL: -.22768708E+02 0.88168723E+03 0.27215626E+02
Reciprocal VIRIAL: 0.12595893E+02 0.27215626E+02 0.91084839E+03
..................
Direct VIRIAL: -.36891153E+13 -.49552687E+13 0.20832023E+13
Direct VIRIAL: -.49552687E+13 -.90665996E+13 0.55269516E+13
Direct VIRIAL: 0.20832023E+13 0.55269516E+13 -.44790569E+13
..................
Dir Sum EE vir trace: 0.28718805E+06
..................
Adjust VIRIAL: -.15848377E+04 0.46048938E+01 -.46608917E+01
Adjust VIRIAL: 0.46048938E+01 -.19356951E+04 -.35057197E+03
Adjust VIRIAL: -.46608917E+01 -.35057197E+03 -.15573200E+04
..................
Recip Disp. VIRIAL: 0.14223011E+04 0.00000000E+00 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.14223011E+04 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.00000000E+00 0.14223011E+04
..................
Self VIRIAL: 0.59405747E-25 0.00000000E+00 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.59405747E-25 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.00000000E+00 0.59405747E-25
..................
Atomic VIRIAL: -.36891153E+13 -.49552687E+13 0.20832023E+13
Atomic VIRIAL: -.49552687E+13 -.90665996E+13 0.55269516E+13
Atomic VIRIAL: 0.20832023E+13 0.55269516E+13 -.44790569E+13
--------------------------------------------
NSTEP = 0 TIME(PS) = 20.000 TEMP(K) = 0.00 PRESS =**********
Etot = ************ EKtot = 0.0000 EPtot = ************
BOND = 1696.8673 ANGLE = 5289.8136 DIHED = 4788.3597
1-4 NB = 2725.5275 1-4 EEL = 38059.6550 VDWAALS = ************
EELEC = -284831.7689 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = ************ VOLUME = 859914.0000
Density = 0.9286
Ewald error estimate: 0.3357E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 0
Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
NET FORCE PER ATOM: 0.1557E-07 0.1994E-06 0.3748E-07
Evdw = ********************
Ehbond = 0.000000000000
Ecoulomb = -284831.768854982570
E polarization = 0.000000000000
Iso virial = ********************
Eevir vs. Ecoulomb = 0.000033574475
E electrostatic (self) = ********************
(rec) = 1158.665097299469
(dir) = -237313.604831216890
(adj) = 982379.728813647870
MOLECULAR VIRIAL: -.40483186E+13 -.43024895E+13 0.18530676E+13
MOLECULAR VIRIAL: -.51988030E+13 -.84055000E+13 0.45371267E+13
MOLECULAR VIRIAL: 0.19878506E+13 0.54599166E+13 -.35002724E+13
--------------------------------------------
Reciprocal VIRIAL: 0.91947519E+03 -.22768708E+02 0.12595893E+02
Reciprocal VIRIAL: -.22768708E+02 0.88168723E+03 0.27215626E+02
Reciprocal VIRIAL: 0.12595893E+02 0.27215626E+02 0.91084839E+03
..................
Direct VIRIAL: -.36891153E+13 -.49552687E+13 0.20832023E+13
Direct VIRIAL: -.49552687E+13 -.90665996E+13 0.55269516E+13
Direct VIRIAL: 0.20832023E+13 0.55269516E+13 -.44790569E+13
..................
Dir Sum EE vir trace: 0.28718805E+06
..................
Adjust VIRIAL: -.15848377E+04 0.46048938E+01 -.46608917E+01
Adjust VIRIAL: 0.46048938E+01 -.19356951E+04 -.35057197E+03
Adjust VIRIAL: -.46608917E+01 -.35057197E+03 -.15573200E+04
..................
Recip Disp. VIRIAL: 0.14223011E+04 0.00000000E+00 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.14223011E+04 0.00000000E+00
Recip Disp. VIRIAL: 0.00000000E+00 0.00000000E+00 0.14223011E+04
..................
Self VIRIAL: 0.59405747E-25 0.00000000E+00 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.59405747E-25 0.00000000E+00
Self VIRIAL: 0.00000000E+00 0.00000000E+00 0.59405747E-25
..................
Atomic VIRIAL: -.36891153E+13 -.49552687E+13 0.20832023E+13
Atomic VIRIAL: -.49552687E+13 -.90665996E+13 0.55269516E+13
Atomic VIRIAL: 0.20832023E+13 0.55269516E+13 -.44790569E+13
--------------------------------------------
vlimit exceeded for step 0; vmax = 69638362427.85799
Number of grids per unit cell in each dimension:
793 913 931
Unit cell edge lengths in each dimension:
3437.756 3957.416 4037.364
Distance between parallel faces of unit cell:
3437.756 3957.416 4037.364
Distance between faces of short range grid subcells:
4.335 4.335 4.337
Resulting cutoff from subcell neighborhoods is 13.004
EWALD BOMB in subroutine ewald_list
volume of ucell too big!!
a regular restart should fix things
Received on Mon Dec 18 2000 - 07:53:12 PST