--------------------------------------- GIBBS Version 5 AMBER/UCSF(1997) -------------------------------------- [-O]verwriting output File Assignments: ----------------- |PIN : gib01.in |POUT : gib_cs_k.out |PCOORD : PCOORD |PVEL : PVEL |PEN : PEN |PPARM : ../setup/crown_k_cs.top |PINCRD : gib_cs.rst |PREFC : PREFC |PREST : gib_cs_k.rst |PINFO : PINFO |MICSTAT : MICSTAT |CONSTMAT: CONSTMAT |CNSTSCRT: CNSTSCRT |PATNRG : PATNRG Here is the input file: # Thermodynamic integration with dynamic windows # starting from equilibrated system # in vacuum, distance-dependent dielectric # all solute-solute interactions, no pairlist calc &cntrl irest=0, ntx=5, init=4, nstlim=-1, dt=0.002, nscm=1000, ntt=1, ntc=2, ntf=2, tol=0.000005, ntb=0, temp0=10.0, idiel=0, scee=2.0, iftres=0, nsnb=999999, almda=0.0, isldyn=2, idifrg=1, nstmeq=100, nstmul=200, ntpr=1000, &end ------------------------------------------------------------------------------- READING MOLECULAR TOPOLOGY FILE (PPARM) -------------------- DYNAMIC MEMORY ALLOCATED USED | INTEGER: 3750000 2512 | REAL: 1500000 3322 | CHARACTER: 125000 308 | AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 3747488 MAXIMUM N-B PAIRS -------------------- Title line from parm: CONTROL FLAGS FOR THIS RUN -------------------------- # Thermodynamic integration with dynamic windows THE TIME LIMIT FOR THE JOB = 1000000. THE RESTART PARAMETER = 0 (irest ) THE FLAG FOR BELLY OPTION = 0 (ibelly) THE FLAG FOR DNA CHARGE CHANGE = 0 (ichdna) THE FLAG FOR POLARIZATION = 0 (ipol ) THE FLAG FOR 3bods = 0 (i3bod ) # of atoms = 43 NSM = 0 NRAM = 0 NTX = 5 NTXO = 1 ISEED = 71277 TempI = 0.000 HEAT = 0.000 NTB = 0 IFTRES= 0 BOXX = 0.000 BOXY = 0.000 BOXZ = 0.000 BETA = 0.000 NRUN = 1 NTT = 1 TEMP0 = 10.000 DTEMP = 10.000 TAUTP = 0.200 TAUTS = 0.200 ISOLVP= 0 NSEL = 0 DTUSE = 1.000 NTP = 0 NPSCAL= 0 PRES0 = 1.000 COMP = 44.600 TAUP = 0.200 NTCM = 0 NSCM = 1000 ISVAT = 1 NSTLIM=******* INIT = 4 T = 0.00000 DT = 0.00200 VLIMIT= 0.000 IVEMAX= 0 NTC = 2 TOL = 0.00001 TOLR2 = 0.00010 NCORC = 0 ISHKFL= 1 ITIMTH= 0 JFASTW= 0 NTF = 2 NTID = 0 NTNB = 1 NSNB =***** IDIEL = 0 IELPER= 0 IMGSLT= 0 IDSX0 = 0 ITRSLU= 1 IOLEPS= 0 INTPRT= 0 ITIP = 0 CUT = 8.00000 SCNB = 2.00000 SCEE = 2.00000 DIELC = 1.00000 CUT2ND= 0.00000 CUTPRT= 0.00000 NTPR = 1000 NTWX = -1 NTWV = -1 NTWE = -1 NTWXM = 999999 NTWVM = 999999 NTWEM = 999999 IOUTFM= 0 ISANDE= 0 IPERAT= 0 IATCMP= 0 NTATDP= 0 ICMPDR= 0 NCMPDR= 0 NTWPRT= 0 NTWPR0= 0 NTR = 0 NRC = 0 NTRX = 1 TAUR = 1.000 INTR = 0 IBIGM = 1 IDUM1 = 0 NMRMAX= 0 IWTMAX = 0 ISFTRP= 0 RWELL = 5.00000 IFTIME= 1 CTIMT = 0.00000 ALMDA = 0.0000000 ALMDEL = 0.0001000 ISLDYN= 2 IDIFRG= 1 NSTMEQ= 100 NSTMUL= 200 NDMPMC= 0 IDWIDE= 0 IBNDLM= 0 IFTIME= 0 CTIMT = -------------------- DYNAMICALLY MODIFIED WINDOWS REQUESTED IAVSLP= 8 IAVSLM= 2 ISLP = 1 CORRSL= 0.8000000 AMXMOV= 0.10000 IAVDEL= -1 IAVDEM= 2 AMXDEL= 1.0000000 ALMDL0= 0.1000000E-03 DLMIN = 0.1000000E-05 DLMAX = 0.1000000 AMXRST= 0.5000000 NORSTS= 0 NTSD = 1000 -------------------- NSTPE = 2 NSTPA = 2 DTE = 0.00100 DTA = 0.00100 IVCAP = 0 MATCAP= 0 IFCAP = 0 NATCAP= 0 CUTCAP= 0.00000 XCAP = 0.00000 YCAP = 0.00000 ZCAP = 0.00000 FCAP = 1.50000 Water definition for fast 3pt model: Resname = WAT ; Oxygen_name = O ; Hyd_name1 = H1 ; Hyd_name2 = H2 ------------------ CALCULATION METHOD Dynamically Modified Interval Thermodynamic Integration ------------------ READING ATOMIC COORDINATES AND VELOCITIES ----------------------------------------- Title: # Using gibbs for MD of the perturbed state Number of triangulated 3-point waters found: 0 Solute/solvent pointers: IPTSOL= 7 NATRCM= 43 IPTRES= 7 IPTATM= 43 NSPSOL= 0 NSPSTR= 0 NSOLUT= 43 NATOM = 43 | Total accumulated time: 0.07 (seconds) / 0.00 (hours) %GIBBS-I-NEWRUN, Begining NRUN = 1 nb-update: total= 693 hbpair= 0 pert= 42 NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 96.876 PRESS = 0.00 Etotal = 45.60171 Kinetic = 9.52933 Potential = 36.07238 Bond = 0.76462 Angle = 2.16737 Dihed = 4.66279 1-4 VdW = 4.66955 1-4 Elec= 30.56255 Van d Waal = 13.43616 Elect. = -20.19068 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 0.000000 Last F.E. update: Lambda = 0.000000 Step = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 11.665 PRESS = 0.00 Etotal = 17.97211 Kinetic = 1.14745 Potential = 16.82466 Bond = 0.37845 Angle = 2.59805 Dihed = 3.74446 1-4 VdW = 4.43144 1-4 Elec= 30.02346 Van d Waal = -4.08710 Elect. = -20.26410 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 0.023426 Last F.E. update: Lambda = 0.000200 Step = 900 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.000200 F_energy = -0.00048 ELEC = 0.000 NONB = 0.000 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 0.000000-->0.023426 NWINDOWS= 3 delta(LAMBDA)=0.7808754E-02 dA/d(LAMBDA) [SLOPE]= 3.3559 slope*delta(LAMBDA)= 0.28160E-01 corr. coef.= 0.954991 pts for line= 2.50 delA(for)-delA(rev)= 0.27013E-03 multiplier= 1.0000 delta(free energy): 0.16042E-03 max. dA= -0.43055E-03 min. dA= -0.50717E-04 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 0 NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 7.533 PRESS = 0.00 Etotal = 17.91016 Kinetic = 0.74101 Potential = 17.16915 Bond = 0.48463 Angle = 3.03222 Dihed = 3.87108 1-4 VdW = 4.07813 1-4 Elec= 29.87517 Van d Waal = -3.99910 Elect. = -20.17297 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 0.264984 Last F.E. update: Lambda = 0.164984 Step = 1800 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.164984 F_energy = -0.02054 ELEC = -0.021 NONB = 0.000 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 0.023426-->0.264984 NWINDOWS= 3 delta(LAMBDA)=0.8051909E-01 dA/d(LAMBDA) [SLOPE]= 0.18556 slope*delta(LAMBDA)= 0.13681E-01 corr. coef.= 0.988298 pts for line= 5.00 delA(for)-delA(rev)= 0.28456E-02 multiplier= 1.0000 delta(free energy): 0.66852E-02 max. dA= -0.85875E-02 min. dA= -0.56574E-02 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 3 NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 10.214 PRESS = 0.00 Etotal = 17.89902 Kinetic = 1.00468 Potential = 16.89434 Bond = 0.23373 Angle = 2.50219 Dihed = 3.89003 1-4 VdW = 4.66447 1-4 Elec= 30.17469 Van d Waal = -4.27341 Elect. = -20.29737 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 0.564984 Last F.E. update: Lambda = 0.564984 Step = 3000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.564984 F_energy = -0.03410 ELEC = -0.034 NONB = 0.000 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 0.264984-->0.664984 NWINDOWS= 4 delta(LAMBDA)=0.1000000 dA/d(LAMBDA) [SLOPE]= 0.77371E-01 slope*delta(LAMBDA)= 0.77371E-02 corr. coef.= 0.962815 pts for line= 7.75 delA(for)-delA(rev)= 0.16928E-02 multiplier= 1.0000 delta(free energy): 0.33902E-02 max. dA= -0.55351E-02 min. dA= -0.18165E-02 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 4 NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 9.415 PRESS = 0.00 Etotal = 17.88030 Kinetic = 0.92612 Potential = 16.95418 Bond = 0.32821 Angle = 2.32588 Dihed = 3.69088 1-4 VdW = 4.72216 1-4 Elec= 30.23793 Van d Waal = -4.02730 Elect. = -20.32359 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 0.964984 Last F.E. update: Lambda = 0.864984 Step = 3900 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.864984 F_energy = -0.03716 ELEC = -0.037 NONB = 0.000 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 0.664984-->0.964984 NWINDOWS= 3 delta(LAMBDA)=0.1000000 dA/d(LAMBDA) [SLOPE]= 0.32751E-01 slope*delta(LAMBDA)= 0.32751E-02 corr. coef.= 0.944053 pts for line= 8.00 delA(for)-delA(rev)= 0.35533E-03 multiplier= 1.0000 delta(free energy): 0.10215E-02 max. dA= -0.13144E-02 min. dA= -0.75051E-03 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 3 A V E R A G E S O V E R 4500 S T E P S NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 16.222 PRESS = 0.00 Etotal = 18.98387 Kinetic = 1.59567 Potential = 17.38820 Bond = 0.45293 Angle = 2.54615 Dihed = 4.03262 1-4 VdW = 4.50506 1-4 Elec= 29.83087 Van d Waal = -3.76330 Elect. = -20.21612 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 R M S F L U C T U A T I O N S NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 21.283 PRESS = 0.00 Etotal = 4.04230 Kinetic = 2.09355 Potential = 2.25922 Bond = 0.25260 Angle = 0.70157 Dihed = 0.69286 1-4 VdW = 0.34847 1-4 Elec= 0.42833 Van d Waal = 1.39371 Elect. = 0.15820 H-bond = 0.00000 Constraint = 0.00000 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000 Current Lambda = 1.000000 Last F.E. update: Lambda = 1.000000 Step = 4500 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = -0.03791 ELEC = -0.038 NONB = 0.000 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 0.000000-->1.000000 NWINDOWS= 15 delta(LAMBDA)=0.7766557E-01 dA/d(LAMBDA) [SLOPE]= 0.55056 slope*delta(LAMBDA)= 0.10092E-01 corr. coef.= 0.962042 pts for line= 6.50 delA(for)-delA(rev)= 0.11850E-02 multiplier= 1.0000 delta(free energy): 0.25270E-02 max. dA= -0.85875E-02 min. dA= -0.50717E-04 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 12 Routine Sec % ---------------------------- | Pairlist 0.00 0.00 | Nonbond 6.38 41.16 | Bond 0.09 0.58 | Angle 1.48 9.55 | Dihedral 5.17 33.35 | PMF 0.05 0.32 | Constraint 0.95 6.13 | Other 1.38 8.90 | Nonsetup 15.44 99.61 ---------------------------- | Total 15.50 0.00 Hours | Setup wallclock_t 0 seconds | Nonsetup wallclock_t 17 seconds