------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 09/17/2008 at 14:36:56 [-O]verwriting output File Assignments: | MDIN: md2.in | MDOUT: md2.out |INPCRD: md1.rst | PARM: md2.prmtop |RESTRT: md2.rst | REFC: md1.rst | MDVEL: mdvel | MDEN: mden | MDCRD: md2.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: protein: 10 ns MD with restraints on Zn and Glu, His, Asp &cntrl imin = 0, irest = 1, ntx = 5, ntb = 2, taup=2.0, pres0=1.0, ntp=1, cut = 10, ntr = 1, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 1000000, dt = 0.002, ntpr = 2000, ntwx = 2000, ntwr = 20000 / hold Zn fixed 500.0 RES 332 END hold coordinated Asp fixed 500 RES 128 END hold coordinated Glu fixed 500 RES 171 END hold coordinated His fixed 500 RES 299 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 = 30.378 | New format PARM file being parsed. | Version = 1.000 Date = 09/05/08 Time = 11:39:34 NATOM = 27074 NTYPES = 18 NBONH = 24406 MBONA = 2736 NTHETH = 5869 MTHETA = 3727 NPHIH = 11308 MPHIA = 8653 NHPARM = 0 NPARM = 0 NNB = 58108 NRES = 7618 NBONA = 2736 NTHETA = 3727 NPHIA = 8653 NUMBND = 47 NUMANG = 97 NPTRA = 51 NATYP = 32 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1573520 | Hollerith 170064 | Integer 994469 | Max Pairs 3898656 | nblistReal 324888 | nblist Int 935392 | Total 38263 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 2000, ntrx = 1, ntwr = 20000 iwrap = 0, ntwx = 2000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, 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 = 1000000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 74.411 Box Y = 74.411 Box Z = 74.411 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 80 NFFT2 = 75 NFFT3 = 75 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: hold Zn fixed GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000 GRP 1 RES 332 TO 332 Number of atoms in this group = 1 ----- READING GROUP 2; TITLE: hold coordinated Asp fixed GROUP 2 HAS HARMONIC CONSTRAINTS 500.00000 GRP 2 RES 128 TO 128 Number of atoms in this group = 12 ----- READING GROUP 3; TITLE: hold coordinated Glu fixed GROUP 3 HAS HARMONIC CONSTRAINTS 500.00000 GRP 3 RES 171 TO 171 Number of atoms in this group = 15 ----- READING GROUP 4; TITLE: hold coordinated His fixed GROUP 4 HAS HARMONIC CONSTRAINTS 500.00000 GRP 4 RES 299 TO 299 Number of atoms in this group = 17 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 40.000 ps Number of triangulated 3-point waters found: 7276 | Atom division among processors: | 0 6770 13538 20306 27074 Sum of charges from parm topology file = -0.00000040 Forcing neutrality... | Running AMBER/MPI version on 4 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 56816. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 56816. NUM_NOSHAKE = 0 CORRECTED RNDFP = 56816. | TOTAL # of degrees of freedom (RNDF) = 56816. --------------------------------------------------- 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 = 2438316 | TOTAL SIZE OF NONBOND LIST = 8642670 vlimit exceeded for step 1897; vmax = 22.2403 Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITER, NIT, LL, I and J are : 0 2 994 2020 2021 Note: This is usually a symptom of some deeper problem with the energetics of the system.