------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Sun May 31 22:12:35 2009 File Assignments: | MDIN: mdin | MDOUT: mdout |INPCRD: sodiumChloride.crd | PARM: sodiumChloride.top |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Simple MD &cntrl imin=0, ntx=1, dt=0.001 cut=1000, ntt=0, temp0=0.0, ntb=0, nstlim=5, ntwe=1, ntwx=1, ntpr=1, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once | New format PARM file being parsed. | Version = 1.000 Date = 05/31/09 Time = 22:12:34 NATOM = 6 NTYPES = 2 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 6 NRES = 6 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 2 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 2000000 1708 | Hollerith 400000 44 | Integer 2000000 729589 | Max Nonbonded Pairs: 5400000 | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 1 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0 dielc = 1.00000, cut =1000.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 5, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 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 = 15 | TOTAL SIZE OF NONBOND LIST = 15 COORD 0 8. 0. 0. COORD 1 -8. 0. 0. COORD 2 0. 9. 0. COORD 3 0. -9. 0. COORD 4 0. 0. 10. COORD 5 0. 0. -10. FORCE 0 -1.29712529 -3.42318274 -3.16208078 FORCE 1 1.297629 3.4228312 3.16184174 FORCE 2 -3.0428291 -1.02489548 -2.72722115 FORCE 3 3.04251662 1.02539214 2.7270599 FORCE 4 -2.52966462 -2.45449904 -0.830164431 FORCE 5 2.52947339 2.45435391 0.830564722 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0000 EPtot = -55.8057 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8032 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 8. 0. 0. COORD 1 -8. 0. 0. COORD 2 0. 9. 0. COORD 3 0. -9. 0. COORD 4 0. 0. 10. COORD 5 0. 0. -10. FORCE 0 -1.29712529 -3.42318274 -3.16208078 FORCE 1 1.297629 3.4228312 3.16184174 FORCE 2 -3.0428291 -1.02489548 -2.72722115 FORCE 3 3.04251662 1.02539214 2.7270599 FORCE 4 -2.52966462 -2.45449904 -0.830164431 FORCE 5 2.52947339 2.45435391 0.830564722 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0000 EPtot = -55.8057 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8032 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 7.9999882 -3.11501458E-05 -2.87741803E-05 COORD 1 -7.99999234 2.01993881E-05 1.86591931E-05 COORD 2 -2.76890185E-05 8.99999067 -2.48170615E-05 COORD 3 1.79550117E-05 -8.99999395 1.60933853E-05 COORD 4 -2.30193442E-05 -2.23353554E-05 9.99999245 COORD 5 1.49273545E-05 1.44840468E-05 -9.9999951 FORCE 0 -1.29716171 -3.42317866 -3.16207437 FORCE 1 1.29765761 3.42283029 3.16183716 FORCE 2 -3.04282471 -1.02492962 -2.72721312 FORCE 3 3.04251658 1.02542064 2.72705373 FORCE 4 -2.5296585 -2.45449141 -0.830193465 FORCE 5 2.52947072 2.45434875 0.830590066 NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0.07 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0008 EPtot = -55.8065 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8040 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 7.99995279 -0.000124600509 -0.000115096605 COORD 1 -7.99996937 8.07975419E-05 7.46367186E-05 COORD 2 -0.000110755994 8.99996269 -9.92680998E-05 COORD 3 7.18200463E-05 -8.99997579 6.43734685E-05 COORD 4 -9.20772656E-05 -8.93412826E-05 9.99996978 COORD 5 5.97093866E-05 5.79361263E-05 -9.99998039 FORCE 0 -1.29727096 -3.42316643 -3.16205517 FORCE 1 1.29774345 3.42282757 3.16182344 FORCE 2 -3.04281154 -1.02503205 -2.72718901 FORCE 3 3.04251647 1.02550615 2.72703521 FORCE 4 -2.52964015 -2.45446852 -0.830280568 FORCE 5 2.52946273 2.45433328 0.830666097 NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 0.27 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0033 EPtot = -55.8089 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8065 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 7.99989376 -0.000280350867 -0.000258966924 COORD 1 -7.99993108 0.000181794429 0.000167932414 COORD 2 -0.000249200687 8.99991606 -0.000223352676 COORD 3 0.000161595102 -8.99994554 0.000144840031 COORD 4 -0.00020717343 -0.000201017365 9.99993201 COORD 5 0.000134346002 0.000130356056 -9.99995588 FORCE 0 -1.29745305 -3.42314605 -3.16202315 FORCE 1 1.2978865 3.42282304 3.16180056 FORCE 2 -3.04278958 -1.02520276 -2.72714882 FORCE 3 3.04251627 1.02564866 2.72700434 FORCE 4 -2.52960956 -2.45443037 -0.83042574 FORCE 5 2.52944942 2.45430748 0.830792816 NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 0.61 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0073 EPtot = -55.8130 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8105 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ COORD 0 7.99981113 -0.000498400849 -0.000460384554 COORD 1 -7.99987747 0.000323189996 0.00029854601 COORD 2 -0.000443022698 8.99985077 -0.000397070059 COORD 3 0.000287280178 -8.99990317 0.000257492708 COORD 4 -0.000368307281 -0.000357362909 9.99987912 COORD 5 0.000238837044 0.000231743531 -9.99992157 FORCE 0 -1.29770796 -3.42311751 -3.16197833 FORCE 1 1.29808677 3.42281669 3.16176853 FORCE 2 -3.04275885 -1.02544176 -2.72709256 FORCE 3 3.042516 1.02584818 2.72696111 FORCE 4 -2.52956673 -2.45437696 -0.830628979 FORCE 5 2.52943077 2.45427136 0.830970225 NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 1.09 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0130 EPtot = -55.8187 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8162 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 5 S T E P S NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 0.41 PRESS = 0.0 Etot = -55.8057 EKtot = 0.0049 EPtot = -55.8106 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.0025 EELEC = -55.8081 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 0.40 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0048 EPtot = 0.0048 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0048 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ | Zhou-Berne energy conservation: log10(DeltaE) =-10.92 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Highest rstack allocated: 25 | Highest istack allocated: 174 | Setup wallclock 0 seconds | Nonsetup wallclock 0 seconds