------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 10/05/2006 at 11:43:00 File Assignments: | MDIN: heat.in | MDOUT: heat.out.1 |INPCRD: VSA_DNA_min_all.rst | PARM: VSA_DNA_min_wat.prmtop |RESTRT: VSA_DNA_heat.rst | REFC: VSA_DNA_min_all.rst | MDVEL: mdvel | MDEN: mden | MDCRD: VSA_DNA_heat.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: #we will start the system from a low temperature of 100 K and gradually heat up #Heating up the system equilibration stage 1 &cntrl nmropt = 1, imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1, ntc = 2, ntf = 2, nstlim = 10000, dt = 0.002, ntt = 3, gamma_ln = 1.0, ntpr= 500, ntwr= 1000, ntwx= 1000, tempi = 00.0, temp0= 273.0, ntwprt = 5550, &end &wt type='TEMP0', istep1=0, istep2=500, value1= 0.0, value2= 50.0, &end &wt type='TEMP0', istep1=500, istep2=1000, value1= 50.0, value2=100.0, &end &wt type='TEMP0', istep1=1000, istep2=1500, value1= 100.0, value2=150.0, &end &wt type='TEMP0', istep1=1500, istep2=2000, value1= 150.0, value2=200.0, &end &wt type='TEMP0', istep1=2000, istep2=2500, value1= 200.0, value2=250.0, &end &wt type='TEMP0', istep1=2500, istep2=3000, value1= 250.0, value2=273.0, &end &wt type='TEMP0', istep1=3000, istep2=10000, value1= 273.0, value2=273.0, &end &wt type='END', &end LISTOUT=POUT DISANG=RST.therm Hold the fur-DNA complex fixed 10.0 RES 1 312 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 40.496 | New format PARM file being parsed. | Version = 1.000 Date = 09/21/06 Time = 12:48:56 NATOM = 66782 NTYPES = 22 NBONH = 63796 MBONA = 3074 NTHETH = 5976 MTHETA = 4312 NPHIH = 11090 MPHIA = 7886 NHPARM = 0 NPARM = 0 NNB = 112302 NRES = 20748 NBONA = 3074 NTHETA = 4312 NPHIA = 7886 NUMBND = 64 NUMANG = 136 NPTRA = 61 NATYP = 39 NPHB = 1 IFBOX = 2 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 3758352 | Hollerith 421442 | Integer 1854670 | Max Pairs 9616608 | nblistReal 801384 | nblist Int 2028795 | Total 90003 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 5550, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 10000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 273.00000, tempi = 0.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 99.195 Box Y = 99.195 Box Z = 99.195 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 100 NFFT2 = 100 NFFT3 = 100 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the fur-DNA complex fixed GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000 GRP 1 RES 1 TO 312 Number of atoms in this group = 5550 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TEMP0 0 500 0.000000 50.000000 0 0 TEMP0 500 1000 50.000000 100.000000 0 0 TEMP0 1000 1500 100.000000 150.000000 0 0 TEMP0 1500 2000 150.000000 200.000000 0 0 TEMP0 2000 2500 200.000000 250.000000 0 0 TEMP0 2500 3000 250.000000 273.000000 0 0 TEMP0 3000 10000 273.000000 273.000000 0 0 RESTRAINTS: Requested file redirections: LISTOUT = POUT DISANG = RST.therm Restraints will be read from file: RST.therm Here are comments from the DISANG input file: Number of restraints read = 18 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 20398 | Atom division among processors: | 0 16697 33392 50087 66782 Sum of charges from parm topology file = 0.00000001 Forcing neutrality... | Running AMBER/MPI version on 4 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 5342941 | TOTAL SIZE OF NONBOND LIST = 21583496 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -295255.0716 EKtot = 0.0000 EPtot = -295255.0716 BOND = 1500.9963 ANGLE = 1207.1904 DIHED = 3114.9025 1-4 NB = 1154.2303 1-4 EEL = 10867.5803 VDWAALS = 49165.9270 EELEC = -362265.8985 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1152E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 29.78 PRESS = 0.0 Etot = -251511.4159 EKtot = 4039.8426 EPtot = -255551.2585 BOND = 1599.0662 ANGLE = 1368.2452 DIHED = 3228.1426 1-4 NB = 1172.7762 1-4 EEL = 10864.9372 VDWAALS = 39617.7671 EELEC = -313819.1734 EHBOND = 0.0000 RESTRAINT = 416.9805 EAMBER (non-restraint) = -255968.2390 Ewald error estimate: 0.5323E-05 ------------------------------------------------------------------------------ NMR restraints: Bond = 111.880 Angle = 0.000 Torsion = 0.000 ===============================================================================