------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 9 | Run on 09/24/2006 at 17:27:37 [-O]verwriting output File Assignments: | MDIN: relaxsystem.in | MDOUT: relaxsystem.out | INPCRD: relaxwater_min.rst | PARM: wild.prmtop | RESTRT: relaxsystem_min.rst | REFC: relaxwater_min.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: Hold the shell relax others &cntrl imin = 1, ncyc = 1000, maxcyc = 3000, ntb = 1, ntr = 1 / Hold the 15~20A shell fixed part01 0.5 RES 144 160 END Hold the 15~20A shell fixed part02 0.5 RES 162 163 END Hold the 15~20A shell fixed part03 0.5 RES 166 167 END Hold the 15~20A shell fixed part04 0.5 RES 170 178 END Hold the 15~20A shell fixed part05 0.5 RES 180 181 END Hold the 15~20A shell fixed part06 0.5 RES 183 189 END Hold the 15~20A shell fixed part07 0.5 RES 194 END Hold the 15~20A shell fixed part08 0.5 RES 196 200 END Hold the 15~20A shell fixed part09 0.5 RES 208 210 END Hold the 15~20A shell fixed part10 0.5 RES 212 225 END Hold the 15~20A shell fixed part11 0.5 RES 239 252 END Hold the 15~20A shell fixed part12 0.5 RES 254 255 END Hold the 15~20A shell fixed part13 0.5 RES 259 263 END Hold the 15~20A shell fixed part14 0.5 RES 265 278 END Hold the 15~20A shell fixed part15 0.5 RES 291 296 END Hold the 15~20A shell fixed part16 0.5 RES 298 END Hold the 15~20A shell fixed part17 0.5 RES 308 317 END Hold the 15~20A shell fixed part18 0.5 RES 322 331 END Hold the 15~20A shell fixed part19 0.5 RES 356 366 END Hold the 15~20A shell fixed part20 0.5 RES 382 END Hold the 15~20A shell fixed part21 0.5 RES 386 387 END Hold the 15~20A shell fixed part22 0.5 RES 391 END Hold the 15~20A shell fixed part23 0.5 RES 396 398 END Hold the 15~20A shell fixed part24 0.5 RES 402 412 END Hold the 15~20A shell fixed part25 0.5 RES 426 433 END Hold the 15~20A shell fixed part26 0.5 RES 434 436 END Hold the 15~20A shell fixed part27 0.5 RES 438 445 END Hold the 15~20A shell fixed part28 0.5 RES 457 464 END Hold the 15~20A shell fixed part29 0.5 RES 486 490 END Hold the 15~20A shell fixed part30 0.5 RES 491 493 END Hold the 15~20A shell fixed part31 0.5 RES 497 END Hold the 15~20A shell fixed part32 0.5 RES 499 509 END Hold the 15~20A shell fixed part33 0.5 ERS 521 525 END END | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | MPI | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 30.408 | New format PARM file being parsed. | Version = 1.000 Date = 09/15/06 Time = 10:52:08 | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 27083 NTYPES = 21 NBONH = 24333 MBONA = 2791 NTHETH = 6112 MTHETA = 3773 NPHIH = 11589 MPHIA = 8468 NHPARM = 0 NPARM = 0 NNB = 58377 NRES = 7587 NBONA = 2791 NTHETA = 3773 NPHIA = 8468 NUMBND = 92 NUMANG = 197 NPTRA = 79 NATYP = 60 NPHB = 1 IFBOX = 2 NMXRS = 86 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 14 14 14 | Direct force subcell size = 5.3203 5.3203 5.3203 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 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 = 50, 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 = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 3000, ncyc = 1000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 74.484 Box Y = 74.484 Box Z = 74.484 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 80 NFFT2 = 75 NFFT3 = 75 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the 15~20A shell fixed part01 GROUP 1 HAS HARMONIC CONSTRAINTS 0.50000 GRP 1 RES 144 TO 160 Number of atoms in this group = 247 ----- READING GROUP 2; TITLE: Hold the 15~20A shell fixed part02 GROUP 2 HAS HARMONIC CONSTRAINTS 0.50000 GRP 2 RES 162 TO 163 Number of atoms in this group = 27 ----- READING GROUP 3; TITLE: Hold the 15~20A shell fixed part03 GROUP 3 HAS HARMONIC CONSTRAINTS 0.50000 GRP 3 RES 166 TO 167 Number of atoms in this group = 26 ----- READING GROUP 4; TITLE: Hold the 15~20A shell fixed part04 GROUP 4 HAS HARMONIC CONSTRAINTS 0.50000 GRP 4 RES 170 TO 178 Number of atoms in this group = 92 ----- READING GROUP 5; TITLE: Hold the 15~20A shell fixed part05 GROUP 5 HAS HARMONIC CONSTRAINTS 0.50000 GRP 5 RES 180 TO 181 Number of atoms in this group = 36 ----- READING GROUP 6; TITLE: Hold the 15~20A shell fixed part06 GROUP 6 HAS HARMONIC CONSTRAINTS 0.50000 GRP 6 RES 183 TO 189 Number of atoms in this group = 97 ----- READING GROUP 7; TITLE: Hold the 15~20A shell fixed part07 GROUP 7 HAS HARMONIC CONSTRAINTS 0.50000 GRP 7 RES 194 TO 194 Number of atoms in this group = 17 ----- READING GROUP 8; TITLE: Hold the 15~20A shell fixed part08 GROUP 8 HAS HARMONIC CONSTRAINTS 0.50000 GRP 8 RES 196 TO 200 Number of atoms in this group = 85 ----- READING GROUP 9; TITLE: Hold the 15~20A shell fixed part09 GROUP 9 HAS HARMONIC CONSTRAINTS 0.50000 GRP 9 RES 208 TO 210 Number of atoms in this group = 41 ----- READING GROUP 10; TITLE: Hold the 15~20A shell fixed part10 GROUP 10 HAS HARMONIC CONSTRAINTS 0.50000 GRP 10 RES 212 TO 225 Number of atoms in this group = 174 ----- READING GROUP 11; TITLE: Hold the 15~20A shell fixed part11 GROUP 11 HAS HARMONIC CONSTRAINTS 0.50000 GRP 11 RES 239 TO 252 Number of atoms in this group = 315 ----- READING GROUP 12; TITLE: Hold the 15~20A shell fixed part12 GROUP 12 HAS HARMONIC CONSTRAINTS 0.50000 GRP 12 RES 254 TO 255 Number of atoms in this group = 38 ----- READING GROUP 13; TITLE: Hold the 15~20A shell fixed part13 GROUP 13 HAS HARMONIC CONSTRAINTS 0.50000 GRP 13 RES 259 TO 263 Number of atoms in this group = 81 ----- READING GROUP 14; TITLE: Hold the 15~20A shell fixed part14 GROUP 14 HAS HARMONIC CONSTRAINTS 0.50000 GRP 14 RES 265 TO 278 Number of atoms in this group = 179 ----- READING GROUP 15; TITLE: Hold the 15~20A shell fixed part15 GROUP 15 HAS HARMONIC CONSTRAINTS 0.50000 GRP 15 RES 291 TO 296 Number of atoms in this group = 94 ----- READING GROUP 16; TITLE: Hold the 15~20A shell fixed part16 GROUP 16 HAS HARMONIC CONSTRAINTS 0.50000 GRP 16 RES 298 TO 298 Number of atoms in this group = 16 ----- READING GROUP 17; TITLE: Hold the 15~20A shell fixed part17 GROUP 17 HAS HARMONIC CONSTRAINTS 0.50000 GRP 17 RES 308 TO 317 Number of atoms in this group = 131 ----- READING GROUP 18; TITLE: Hold the 15~20A shell fixed part18 GROUP 18 HAS HARMONIC CONSTRAINTS 0.50000 GRP 18 RES 322 TO 331 Number of atoms in this group = 171 ----- READING GROUP 19; TITLE: Hold the 15~20A shell fixed part19 GROUP 19 HAS HARMONIC CONSTRAINTS 0.50000 GRP 19 RES 356 TO 366 Number of atoms in this group = 169 ----- READING GROUP 20; TITLE: Hold the 15~20A shell fixed part20 GROUP 20 HAS HARMONIC CONSTRAINTS 0.50000 GRP 20 RES 382 TO 382 Number of atoms in this group = 6 ----- READING GROUP 21; TITLE: Hold the 15~20A shell fixed part21 GROUP 21 HAS HARMONIC CONSTRAINTS 0.50000 GRP 21 RES 386 TO 387 Number of atoms in this group = 6 ----- READING GROUP 22; TITLE: Hold the 15~20A shell fixed part22 GROUP 22 HAS HARMONIC CONSTRAINTS 0.50000 GRP 22 RES 391 TO 391 Number of atoms in this group = 3 ----- READING GROUP 23; TITLE: Hold the 15~20A shell fixed part23 GROUP 23 HAS HARMONIC CONSTRAINTS 0.50000 GRP 23 RES 396 TO 398 Number of atoms in this group = 9 ----- READING GROUP 24; TITLE: Hold the 15~20A shell fixed part24 GROUP 24 HAS HARMONIC CONSTRAINTS 0.50000 GRP 24 RES 402 TO 412 Number of atoms in this group = 33 ----- READING GROUP 25; TITLE: Hold the 15~20A shell fixed part25 GROUP 25 HAS HARMONIC CONSTRAINTS 0.50000 GRP 25 RES 426 TO 433 Number of atoms in this group = 24 ----- READING GROUP 26; TITLE: Hold the 15~20A shell fixed part26 GROUP 26 HAS HARMONIC CONSTRAINTS 0.50000 GRP 26 RES 434 TO 436 Number of atoms in this group = 9 ----- READING GROUP 27; TITLE: Hold the 15~20A shell fixed part27 GROUP 27 HAS HARMONIC CONSTRAINTS 0.50000 GRP 27 RES 438 TO 445 Number of atoms in this group = 24 ----- READING GROUP 28; TITLE: Hold the 15~20A shell fixed part28 GROUP 28 HAS HARMONIC CONSTRAINTS 0.50000 GRP 28 RES 457 TO 464 Number of atoms in this group = 24 ----- READING GROUP 29; TITLE: Hold the 15~20A shell fixed part29 GROUP 29 HAS HARMONIC CONSTRAINTS 0.50000 GRP 29 RES 486 TO 490 Number of atoms in this group = 15 ----- READING GROUP 30; TITLE: Hold the 15~20A shell fixed part30 GROUP 30 HAS HARMONIC CONSTRAINTS 0.50000 GRP 30 RES 491 TO 493 Number of atoms in this group = 9 ----- READING GROUP 31; TITLE: Hold the 15~20A shell fixed part31 GROUP 31 HAS HARMONIC CONSTRAINTS 0.50000 GRP 31 RES 497 TO 497 Number of atoms in this group = 3 ----- READING GROUP 32; TITLE: Hold the 15~20A shell fixed part32 GROUP 32 HAS HARMONIC CONSTRAINTS 0.50000 GRP 32 RES 499 TO 509 Number of atoms in this group = 33 ----- READING GROUP 33; TITLE: Hold the 15~20A shell fixed part33 GROUP 33 HAS HARMONIC CONSTRAINTS 0.50000 GRP 33 RES 521 TO 525 Number of atoms in this group = 15 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 7205 Sum of charges from parm topology file = -8.99999837 Assuming uniform neutralizing plasma | Dynamic Memory, Types Used: | Reals 978154 | Integers 1006853 | Nonbonded Pairs Initial Allocation: 771865 | Running AMBER/MPI version on 8 nodes -------------------------------------------------------------------------------- 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 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -9.3640E+04 2.8811E+00 2.3439E+02 N1' 3617 BOND = 6453.9378 ANGLE = 844.3629 DIHED = 3216.6361 VDWAALS = 12926.5591 EEL = -130170.5927 HBOND = 0.0000 1-4 VDW = 1399.7355 1-4 EEL = 11689.4876 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -9.5216E+04 8.6529E-01 1.3887E+02 CG 2385 BOND = 6494.9722 ANGLE = 774.7761 DIHED = 3269.6011 VDWAALS = 12546.5725 EEL = -130875.4135 HBOND = 0.0000 1-4 VDW = 1210.4819 1-4 EEL = 11351.7665 RESTRAINT = 11.0292 EAMBER = -95227.2432 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -9.6265E+04 3.7181E+01 6.6734E+03 O2B 3586 BOND = 6524.5268 ANGLE = 858.4363 DIHED = 3274.2217 VDWAALS = 12568.4294 EEL = -131173.1129 HBOND = 0.0000 1-4 VDW = 1173.8493 1-4 EEL = 10486.6645 RESTRAINT = 22.3939 EAMBER = -96286.9849 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -3.2059E+07 5.2082E+10 9.3600E+12 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 200 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.8550E+07 1.7361E+10 3.1201E+12 O2B 3586 BOND = 6529.2480 ANGLE = 864.5189 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8937 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 350 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.8550E+07 1.7361E+10 3.1201E+12 O2B 3586 BOND = 6529.2480 ANGLE = 864.5189 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8937 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 500 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 550 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.8550E+07 1.7361E+10 3.1201E+12 O2B 3586 BOND = 6529.2480 ANGLE = 864.5189 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8937 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 650 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 750 -1.8550E+07 1.7361E+10 3.1201E+12 O2B 3586 BOND = 6529.2480 ANGLE = 864.5189 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8937 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 800 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 850 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.8550E+07 1.7361E+10 3.1201E+12 O2B 3586 BOND = 6529.2480 ANGLE = 864.5189 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8937 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 950 -4.0054E+07 8.1396E+10 1.4628E+13 O2B 3586 BOND = 6529.2481 ANGLE = 864.5190 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.2505E+07 7.8509E+09 1.4109E+12 H41 3588 BOND = 6529.2486 ANGLE = 864.5196 DIHED = 3274.2378 VDWAALS = 12568.4458 EEL = -131173.8938 HBOND = 0.0000 1-4 VDW = 1173.8426 1-4 EEL = ************* RESTRAINT = 22.5286 EAMBER = ************* .... RESTARTED DUE TO LINMIN FAILURE ...