------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/13/2006 at 16:04:16 [-O]verwriting output File Assignments: | MDIN: no_plug_min_crys_h2o_1.in | MDOUT: /dtemp/barrett/amber8/no_plug_min_crys_h2o_1.out |INPCRD: no_plug_hs_added_gb.inpcrd | PARM: no_plug_hs_added_gb.prmtop |RESTRT: no_plug_min_crys_h2o_1.restrt | REFC: no_plug_hs_added_gb.inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimize crystal waters in no_plug structure, allowing hydrogens to move but ho &cntrl imin=1, ntx=1, ntf=1, ntb=0, cut=35, igb=5, rgbmax=30, ntr=1, ntc=1, maxcyc=500, ntmin=2, restraint_wt=500, restraintmask=:* & !@H= & !:WAT / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 06/06/06 Time = 20:09:30 NATOM = 47782 NTYPES = 20 NBONH = 26999 MBONA = 21203 NTHETH = 46375 MTHETA = 28777 NPHIH = 87282 MPHIA = 61432 NHPARM = 0 NPARM = 0 NNB = 235683 NRES = 4886 NBONA = 21203 NTHETA = 28777 NPHIA = 61432 NUMBND = 63 NUMANG = 134 NPTRA = 72 NATYP = 40 NPHB = 1 IFBOX = 0 NMXRS = 39 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2103849 | Hollerith 291580 | Integer 2264130 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 26419 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 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 = 0, igb = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 35.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500 rdt = 0.00000, rgbmax = 30.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 500, ncyc = 10, ntmin = 2 dx0 = 0.01000, drms = 0.00010 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mask :*; matches 47782 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 2212 | Atom division among processors: | 0 2995 5976 8971 11944 14942 17923 20906 | 23890 26881 29874 32848 35838 38831 41806 44791 | 47782 | Running AMBER/MPI version on 16 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 6.8283E+12 4.3714E+11 3.8864E+13 CD 6756 BOND = 55589.4701 ANGLE = 12184.7419 DIHED = 24774.6027 VDWAALS = ************* EEL = -179753.6450 EGB = -38256.1350 1-4 VDW = 2621189.7868 1-4 EEL = 113699.2076 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 9.1730E+05 1.3416E+04 3.4242E+06 HD3 12636 BOND = 174345.4160 ANGLE = 28653.8199 DIHED = 26425.8649 VDWAALS = 293609.7798 EEL = -180219.9423 EGB = -37637.7214 1-4 VDW = 271288.7903 1-4 EEL = 113477.0466 RESTRAINT = 227361.4291 EAMBER = 689943.0537 NSTEP ENERGY RMS GMAX NAME NUMBER 100 4.4547E+05 6.9362E+00 1.2393E+03 O 46007 BOND = 47119.7552 ANGLE = 20846.2214 DIHED = 26485.7885 VDWAALS = 135952.0145 EEL = -181401.9787 EGB = -39533.9414 1-4 VDW = 15020.6489 1-4 EEL = 112945.2472 RESTRAINT = 308035.9996 EAMBER = 137433.7557 NSTEP ENERGY RMS GMAX NAME NUMBER 150 2.4980E+05 1.7461E+06 4.2159E+08 O 6066 BOND = 45735.4703 ANGLE = 20692.8121 DIHED = 26462.4725 VDWAALS = 134414.5911 EEL = -375408.3124 EGB = -39394.8692 1-4 VDW = 14967.6163 1-4 EEL = 112961.8468 RESTRAINT = 309363.3886 EAMBER = -59568.3725 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -3.4515E+07 5.6761E+10 1.3704E+13 H1 42216 BOND = 45735.6920 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7849 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2576 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 250 -9.5787E+07 4.3009E+11 1.0384E+14 H1 42216 BOND = 45735.6913 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7842 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2580 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.6168E+08 1.2207E+12 2.9472E+14 H1 42216 BOND = 45735.6911 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7840 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2581 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 350 -3.4515E+07 5.6761E+10 1.3704E+13 H1 42216 BOND = 45735.6920 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7849 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2576 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 400 -9.5787E+07 4.3009E+11 1.0384E+14 H1 42216 BOND = 45735.6913 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7842 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2580 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.6168E+08 1.2207E+12 2.9472E+14 H1 42216 BOND = 45735.6911 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7840 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2581 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.4515E+07 5.6761E+10 1.3704E+13 H1 42216 BOND = 45735.6920 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7849 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2576 EAMBER = ************* Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.4515E+07 5.6761E+10 1.3704E+13 H1 42216 BOND = 45735.6920 ANGLE = 20692.8141 DIHED = 26462.4721 VDWAALS = 134414.7849 EEL = ************* EGB = -39394.8690 1-4 VDW = 14967.6169 1-4 EEL = 112961.8460 RESTRAINT = 309363.2576 EAMBER = ************* -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Calc gb radii 618.83 (16.72% of Gen B) | Communicate gb radii 43.92 ( 1.19% of Gen B) | Calc gb diag 1385.08 (37.43% of Gen B) | Calc gb off-diag 1652.49 (44.66% of Gen B) | Gen Born time 3700.48 (100.0% of Nonbo) | Nonbond force 3700.48 (99.33% of Force) | Bond/Angle/Dihedral 2.95 ( 0.08% of Force) | FRC Collect time 4.81 ( 0.13% of Force) | Other 17.14 ( 0.46% of Force) | Force time 3725.38 (100.0% of Runmd) | Runmd Time 3725.38 (99.89% of Total) | Other 4.08 ( 0.11% of Total) | Total time 3729.55 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 16:04:16.267 on 06/13/2006 | Setup done at 16:04:18.195 on 06/13/2006 | Run done at 17:06:25.826 on 06/13/2006 | wallclock() was called 10008 times