--------------------------------------- GIBBS Version 5 AMBER/UCSF(1997) -------------------------------------- [-O]verwriting output File Assignments: ----------------- |PIN : gib10.in |POUT : gib_na_k.out |PCOORD : PCOORD |PVEL : PVEL |PEN : PEN |PPARM : ../setup/crown_na_k.top |PINCRD : ../dynamics/equipartition/md_na_a.rst |PREFC : PREFC |PREST : gib_na_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=0.0005, nscm=201000, ntt=-201000, dtemp=100, ntc=1, ntf=1, tol=0.000005, ntb=0, temp0=300.0, idiel=0, scee=2.0, iftres=0, nsnb=999999, idifrg=1, isldyn=-2, nstmeq=1000, nstmul=200000, 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 =***** TEMP0 = 300.000 DTEMP = 100.000 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 = 201000 ISVAT = 1 NSTLIM=******* INIT = 4 T = 0.00000 DT = 0.00050 VLIMIT= 0.000 IVEMAX= 0 NTC = 1 TOL = 0.00001 TOLR2 = 0.00010 NCORC = 0 ISHKFL= 1 ITIMTH= 0 JFASTW= 0 NTF = 1 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 = 1.0000000 ALMDEL = 0.0001000 ISLDYN= -2 IDIFRG= 1 NSTMEQ= 1000 NSTMUL= 200000 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: 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: 0.05 (seconds) / 0.00 (hours) %GIBBS-I-NEWRUN, Begining NRUN = 1 nb-update: total= 693 hbpair= 0 pert= 42 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 375.860 PRESS = 0.00 Etotal = 60.13261 Kinetic = 45.93475 Potential = 14.19786 Bond = 13.75332 Angle = 18.88646 Dihed = 9.61727 1-4 VdW = 6.45713 1-4 Elec= 31.62941 Van d Waal = 3.63779 Elect. = -69.78352 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 = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 255.072 PRESS = 0.00 Etotal = 44.52058 Kinetic = 31.17297 Potential = 13.34761 Bond = 15.81451 Angle = 17.91127 Dihed = 9.92817 1-4 VdW = 7.56604 1-4 Elec= 33.00509 Van d Waal = 2.64808 Elect. = -73.52554 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 = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 2000 TIME(PS) = 1.000 TEMP(K) = 242.234 PRESS = 0.00 Etotal = 40.92563 Kinetic = 29.60392 Potential = 11.32171 Bond = 14.07630 Angle = 18.52572 Dihed = 7.26562 1-4 VdW = 6.98813 1-4 Elec= 32.85827 Van d Waal = -0.94688 Elect. = -67.44546 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 = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 3000 TIME(PS) = 1.500 TEMP(K) = 338.507 PRESS = 0.00 Etotal = 55.60348 Kinetic = 41.36966 Potential = 14.23382 Bond = 15.10536 Angle = 15.89092 Dihed = 11.95550 1-4 VdW = 6.99360 1-4 Elec= 31.31636 Van d Waal = 0.28318 Elect. = -67.31109 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 = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 4000 TIME(PS) = 2.000 TEMP(K) = 255.620 PRESS = 0.00 Etotal = 44.07828 Kinetic = 31.23994 Potential = 12.83834 Bond = 12.07553 Angle = 20.39307 Dihed = 9.92757 1-4 VdW = 6.82497 1-4 Elec= 32.11414 Van d Waal = 0.03922 Elect. = -68.53615 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 = 0 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 1.000000 F_energy = 0.00000 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ ....many, many intermediate results deleted ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21099000 TIME(PS) = 10549.500 TEMP(K) = 274.277 PRESS = 0.00 Etotal = 54.96612 Kinetic = 33.52003 Potential = 21.44609 Bond = 12.15196 Angle = 19.35276 Dihed = 4.81517 1-4 VdW = 6.72643 1-4 Elec= 30.75040 Van d Waal = 4.56492 Elect. = -56.91556 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21100000 TIME(PS) = 10550.000 TEMP(K) = 341.854 PRESS = 0.00 Etotal = 54.87461 Kinetic = 41.77873 Potential = 13.09588 Bond = 10.25091 Angle = 15.79209 Dihed = 6.49453 1-4 VdW = 3.87505 1-4 Elec= 29.17351 Van d Waal = 3.51504 Elect. = -56.00523 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21101000 TIME(PS) = 10550.500 TEMP(K) = 274.616 PRESS = 0.00 Etotal = 54.99806 Kinetic = 33.56142 Potential = 21.43664 Bond = 14.32359 Angle = 16.70412 Dihed = 4.35548 1-4 VdW = 8.35684 1-4 Elec= 30.58834 Van d Waal = 5.18166 Elect. = -58.07339 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21102000 TIME(PS) = 10551.000 TEMP(K) = 317.320 PRESS = 0.00 Etotal = 54.95368 Kinetic = 38.78035 Potential = 16.17334 Bond = 12.38246 Angle = 17.00770 Dihed = 6.16866 1-4 VdW = 3.92684 1-4 Elec= 29.51366 Van d Waal = 3.28059 Elect. = -56.10657 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21103000 TIME(PS) = 10551.500 TEMP(K) = 256.184 PRESS = 0.00 Etotal = 55.05517 Kinetic = 31.30883 Potential = 23.74634 Bond = 11.16986 Angle = 22.75132 Dihed = 4.85165 1-4 VdW = 7.09867 1-4 Elec= 30.01591 Van d Waal = 3.77805 Elect. = -55.91912 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT NSTEP = 21104000 TIME(PS) = 10552.000 TEMP(K) = 326.416 PRESS = 0.00 Etotal = 54.87910 Kinetic = 39.89202 Potential = 14.98708 Bond = 10.88331 Angle = 16.52312 Dihed = 5.20680 1-4 VdW = 4.81793 1-4 Elec= 29.60416 Van d Waal = 4.89401 Elect. = -56.94225 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 = 0.002489 Step = 20904000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.002489 F_energy = -9.73186 (Note: values are unchanged from last report) ------------------------------------------------------------------------------ NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT A V E R A G E S O V E R 21105000 S T E P S NSTEP = 21105000 TIME(PS) = 10552.500 TEMP(K) = 294.672 PRESS = 0.00 Etotal = 52.72531 Kinetic = 36.01255 Potential = 16.71275 Bond = 12.84752 Angle = 18.33243 Dihed = 7.19784 1-4 VdW = 6.54202 1-4 Elec= 30.87236 Van d Waal = 1.25314 Elect. = -60.33255 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 = 21105000 TIME(PS) = 10552.500 TEMP(K) = 29.088 PRESS = 0.00 Etotal = 3.77378 Kinetic = 3.55485 Potential = 4.05394 Bond = 2.58673 Angle = 2.88665 Dihed = 2.02838 1-4 VdW = 1.28982 1-4 Elec= 0.93300 Van d Waal = 1.77023 Elect. = 4.56480 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 = 21105000 Method = T.I. Accumulated "forward" quantities (Regular) Lambda = 0.000000 F_energy = -9.74182 ELEC = 0.000 NONB = -9.742 14NB = 0.000 14EL = 0.000 BADH = 0.000 ------------------------------------------------------------------------------ DYNAMICALLY MODIFIED WINDOW STATISTICS: Averages (Abs. values); Lambda Interval: 1.000000-->0.000000 NWINDOWS= 105 delta(LAMBDA)=0.9846017E-02 dA/d(LAMBDA) [SLOPE]= 10.334 slope*delta(LAMBDA)= 0.98173E-01 corr. coef.= 0.999533 pts for line= 7.80 delA(for)-delA(rev)= 0.46011E-02 multiplier= 1.0000 delta(free energy): 0.92779E-01 max. dA= -0.14689 min. dA= -0.11607E-02 # Restarts due to AMXRST= 0 # Steps set to DLMIN= 0 DLMAX= 0 Routine Sec % ---------------------------- | Pairlist 0.02 0.00 | Nonbond 23674.96 45.07 | Bond 945.22 1.80 | Angle 6000.42 11.42 | Dihedral 18958.90 36.10 | PMF 159.10 0.30 | Constraint 0.00 0.00 | Other 2785.58 5.30 | Nonsetup 52524.14 100.00 ---------------------------- | Total 52524.19 14.59 Hours | Setup wallclock_t 0 seconds | Nonsetup wallclock_t 149847 seconds