 | |||||||||||||||
 |
 |
 |
|
 |
|
 |
|
 |
|
 |
|
 |
|
 |
 |
AMBER Archive (2000)
Subject: EWALD BOMB
From: Grzegorz Jezierski (gj_at_mol.uj.edu.pl)
Date: Mon Dec 18 2000 - 09:53:12 CST
- Next message: Jake Isaacs: "initial density generated by solvatebox"
- Previous message: Sanjeev B.S.: "sizes.h for sander"
- Next in thread: darden: "Re: EWALD BOMB"
- Reply: darden: "Re: EWALD BOMB"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Dear AMBER users,
I had performed 20 ps-MD of a 78000 atom system.
I used PBC, no pressure control, and PME.
Then, I have restarted the calculation, and got (after 1 MD iteration) a
message, like:
"Ewald bomb in subroutine 'ewald_list'
volume of ucell too big"
At the first sight, the solute structure (protein) seems OK, but several water
molecules 'flew out' of the box.
I attach the output file from the last - unfinished - run ('dyn.out') as well as
the beginning and the end of the previous run ('dyn0.out').
Thank you for any help.
Regards,
-- ******************************** Grzegorz JezierskiBiophysics 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
- Next message: Jake Isaacs: "initial density generated by solvatebox"
- Previous message: Sanjeev B.S.: "sizes.h for sander"
- Next in thread: darden: "Re: EWALD BOMB"
- Reply: darden: "Re: EWALD BOMB"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
|
VU Home |
VUMC Home |
People Finder |
University Calendar
webmaster- modified on January 30, 2009 |