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| ------------------------------------------------------- | |
| Amber 12 SANDER 2012 | |
| ------------------------------------------------------- | |
| | PMEMD implementation of SANDER, Release 12 | |
| | Run on 02/19/2015 at 01:02:13 | |
| [-O]verwriting output | |
| File Assignments: | |
| | MDIN: min.in | |
| | MDOUT: min3.out | |
| | INPCRD: min3.crd | |
| | PARM: penta.top | |
| | RESTRT: md3.crd | |
| | REFC: min3.crd | |
| | MDVEL: mdvel | |
| | MDEN: mden | |
| | MDCRD: mdcrd | |
| | MDINFO: min3.inf | |
| |LOGFILE: logfile | |
| Here is the input file: | |
| Basic minimisation, weakly restraining backbone | |
| &cntrl | |
| imin=1, maxcyc=500, | |
| ntpr=50, | |
| ntr=1, | |
| ntb=0, cut=25.0, igb=2, | |
| &end | |
| Atoms to be restrained | |
| 0.1 | |
| FIND | |
| CA * * * | |
| N * * * | |
| C * * * | |
| O * * * | |
| SEARCH | |
| RES 1 999 | |
| END | |
| END | |
| | Conditional Compilation Defines Used: | |
| | DIRFRC_COMTRANS | |
| | DIRFRC_EFS | |
| | DIRFRC_NOVEC | |
| | MPI | |
| | PUBFFT | |
| | FFTLOADBAL_2PROC | |
| | BINTRAJ | |
| | MKL | |
| | New format PARM file being parsed. | |
| | Version = 1.000 Date = 12/09/11 Time = 18:38:33 | |
| | Note: 1-4 EEL scale factors are being read from the topology file. | |
| | Note: 1-4 VDW scale factors are being read from the topology file. | |
| | Duplicated 0 dihedrals | |
| | Duplicated 0 dihedrals | |
| -------------------------------------------------------------------------------- | |
| 1. RESOURCE USE: | |
| -------------------------------------------------------------------------------- | |
| NATOM = 59 NTYPES = 7 NBONH = 30 MBONA = 28 | |
| NTHETH = 64 MTHETA = 38 NPHIH = 124 MPHIA = 106 | |
| NHPARM = 0 NPARM = 0 NNB = 296 NRES = 7 | |
| NBONA = 28 NTHETA = 38 NPHIA = 106 NUMBND = 8 | |
| NUMANG = 16 NPTRA = 20 NATYP = 7 NPHB = 0 | |
| IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0 | |
| NCOPY = 0 | |
| Implicit solvent radii are Bondi radii (bondi) | |
| -------------------------------------------------------------------------------- | |
| 2. CONTROL DATA FOR THE RUN | |
| -------------------------------------------------------------------------------- | |
| ACE | |
| 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 = 2, nsnb = 25 | |
| ipol = 0, gbsa = 0, iesp = 0 | |
| dielc = 1.00000, cut = 25.00000, intdiel = 1.00000 | |
| saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000 | |
| gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 | |
| rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 | |
| alpb = 0 | |
| Frozen or restrained atoms: | |
| ibelly = 0, ntr = 1 | |
| restraint_wt = 0.00000 | |
| Energy minimization: | |
| maxcyc = 500, ncyc = 10, ntmin = 1 | |
| dx0 = 0.01000, drms = 0.00010 | |
| | Intermolecular bonds treatment: | |
| | no_intermolecular_bonds = 1 | |
| | Energy averages sample interval: | |
| | ene_avg_sampling = 1 | |
| LOADING THE CONSTRAINED ATOMS AS GROUPS | |
| 5. REFERENCE ATOM COORDINATES | |
| default_name | |
| ----- READING GROUP 1; TITLE: | |
| Atoms to be restrained | |
| GROUP 1 HAS HARMONIC CONSTRAINTS 0.10000 | |
| ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW | |
| GRAPH NAME = CA SYMBOL = * TREE SYMBOL = * RESIDUE TYPE = * | |
| GRAPH NAME = N SYMBOL = * TREE SYMBOL = * RESIDUE TYPE = * | |
| GRAPH NAME = C SYMBOL = * TREE SYMBOL = * RESIDUE TYPE = * | |
| GRAPH NAME = O SYMBOL = * TREE SYMBOL = * RESIDUE TYPE = * | |
| GRP 1 RES 1 TO 7 | |
| Number of atoms in this group = 23 | |
| ----- END OF GROUP READ ----- | |
| -------------------------------------------------------------------------------- | |
| 3. ATOMIC COORDINATES AND VELOCITIES | |
| -------------------------------------------------------------------------------- | |
| default_name | |
| begin time read from input coords = 0.000 ps | |
| Number of triangulated 3-point waters found: 0 | |
| | Dynamic Memory, Types Used: | |
| | Reals 2801 | |
| | Integers 105917 | |
| | Running AMBER/MPI version on 2 nodes | |
| -------------------------------------------------------------------------------- | |
| 4. RESULTS | |
| -------------------------------------------------------------------------------- | |
| NSTEP ENERGY RMS GMAX NAME NUMBER | |
| 1 2.2156E+09 5.8056E+09 4.8494E+10 N 47 | |
| BOND = 12806.6359 ANGLE = 2201.2061 DIHED = 54.9905 | |
| VDWAALS = 43066736.6699 EEL = -255.5723 EGB = -91.1485 | |
| 1-4 VDW = ************* 1-4 EEL = 192.3848 RESTRAINT = 0.0000 | |
| .... RESTARTED DUE TO LINMIN FAILURE ... | |
| NSTEP ENERGY RMS GMAX NAME NUMBER | |
| 50 4.8821E+22 1.2779E+12 1.1337E+13 N 17 | |
| BOND = ************* ANGLE = 4205.9858 DIHED = 103.4246 | |
| VDWAALS = 950.9624 EEL = -154.1826 EGB = -286.8432 | |
| 1-4 VDW = 487.9232 1-4 EEL = 112.3784 RESTRAINT = ************* | |
| EAMBER = ************* | |
| .... RESTARTED DUE TO LINMIN FAILURE ... | |
| .... RESTARTED DUE TO LINMIN FAILURE ... | |
| .... RESTARTED DUE TO LINMIN FAILURE ... | |
| .... RESTARTED DUE TO LINMIN FAILURE ... | |
| FINAL RESULTS | |
| NSTEP ENERGY RMS GMAX NAME NUMBER | |
| 94 1.4805E+19 6.4990E+09 2.6821E+10 CB 31 | |
| BOND = ************* ANGLE = 13019.7142 DIHED = 95.6469 | |
| VDWAALS = 0.0000 EEL = 0.0000 EGB = -710.0129 | |
| 1-4 VDW = -0.0000 1-4 EEL = 0.0001 RESTRAINT = ************* | |
| EAMBER = ************* | |
| ***** REPEATED LINMIN FAILURE ***** | |
| -------------------------------------------------------------------------------- | |
| 5. TIMINGS | |
| -------------------------------------------------------------------------------- | |
| | NonSetup CPU Time in Major Routines, Average for All Tasks: | |
| | | |
| | Routine Sec % | |
| | ------------------------------ | |
| | DataDistrib 0.00 18.75 | |
| | Nonbond 0.01 50.00 | |
| | Bond 0.00 0.00 | |
| | Angle 0.00 15.62 | |
| | Dihedral 0.00 9.38 | |
| | Shake 0.00 0.00 | |
| | Other 0.00 6.24 | |
| | ------------------------------ | |
| | Total 0.02 | |
| | Generalized Born CPU Time, Average for All Tasks: | |
| | | |
| | Routine Sec % | |
| | ------------------------------------ | |
| | Radii Calc 0.00 9.38 | |
| | Diagonal Calc 0.00 18.75 | |
| | Off Diagonal Calc 0.00 9.37 | |
| | GBSA LCPO Calc 0.00 0.00 | |
| | Radii Distrib 0.00 3.13 | |
| | --------------------------------- | |
| | Total 0.01 40.63 | |
| | Master Setup CPU time: 0.27 seconds | |
| | Master NonSetup CPU time: 0.01 seconds | |
| | Master Total CPU time: 0.28 seconds 0.00 hours | |
| | Master Setup wall time: 0 seconds | |
| | Master NonSetup wall time: 0 seconds | |
| | Master Total wall time: 0 seconds 0.00 hours |
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