[-O]verwriting output File Assignments: | MDIN: pvcl20_min.in | MDOUT: pvcl20_min.out |INPCRD: pvcl20_wat.inpcrd | PARM: pvcl20_wat.prmtop |RESTRT: pvcl20_min.rst7 | REFC: pvcl20.inpcrd | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: Minimize &cntrl imin=1, ntb=0, ntx=1, irest=0, maxcyc=2000, ncyc=1000, ntpr=100, ntwx=0, cut=999.0, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 42.268 | New format PARM file being parsed. | Version = 1.000 Date = 04/02/21 Time = 13:10:23 NATOM = 1550 NTYPES = 7 NBONH = 990 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 1880 NRES = 350 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 2 NUMANG = 0 NPTRA = 0 NATYP = 7 NPHB = 0 IFBOX = 2 NMXRS = 28 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 122703 | Hollerith 5002 | Integer 50934 | Max Pairs 1200475 | nblistReal 18600 | nblist Int 2196587 | Total 14592 kbytes | 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 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 100, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 2000, ncyc = 1000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 330 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 1199485 | TOTAL SIZE OF NONBOND LIST = 1199485 NSTEP ENERGY RMS GMAX NAME NUMBER 1 NaN NaN 4.7320E+01 O 756 BOND = 0.0159 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = NaN EEL = NaN HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 ... RESTARTED DUE TO LINMIN FAILURE ... ... RESTARTED DUE TO LINMIN FAILURE ... ... RESTARTED DUE TO LINMIN FAILURE ... ... RESTARTED DUE TO LINMIN FAILURE ... ... RESTARTED DUE TO LINMIN FAILURE ... ***** REPEATED LINMIN FAILURE ***** ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO ***** FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1021 NaN NaN 0.0000E+00 C1 1 BOND = NaN ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000