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LOGs for ID: 22062011140762491

output from eigenvector calculation:


STDOUT:
CUTOFF set to default value (CUTOFF=8) Build Tirion matrix: Pdbmat> Computes the Hessian matrix, using an Elastic Network Model. Pdbmat> Version 3.50, Fevrier 2004. Pdbmat> Options to be read in pdbmat.dat file. Pdbmat> Coordinate filename = 22062011140762491.atom Pdbmat> Distance cutoff = 8.00 Force constant = 10.00 Origin of mass values = CONS Pdbmat> Levelshift = 1.0E-09 PRINTing level = 2 Pdbmat> Coordinate file 22062011140762491.atom to be opened. Openam> File opened: 22062011140762491.atom Pdbmat> Coordinate file in PDB format. Rdatompdb> Reading pdb file. Rdatompdb> End of file reached. Rdatompdb> Number of I/O errors: 0 Rdatompdb> Number of residues found = 2136 First residue number = 29 Last residue number = 87 Number of atoms found = 34417 Mean number per residue = 16.1 Pdbmat> Coordinate statistics: = 70.207242 +/- 20.388280 From: 18.283000 To: 133.158000 = 73.197207 +/- 20.832961 From: 14.987000 To: 120.943000 = 65.227925 +/- 27.494961 From: 5.262000 To: 133.980000 Pdbmat> Masses are all set to one. Openam> File opened: pdbmat.xyzm Pdbmat> Coordinates and masses considered are saved. Openam> File opened: pdbmat.sdijb Pdbmat> Matrix statistics: Pdbmat> The matrix is 2.4806 % Filled. Pdbmat> 25685651 non-zero elements. Pdbmat> 2831491 atom-atom interactions. Pdbmat> Number per atom= 164.54 +/- 42.36 Maximum number = 248 Minimum number = 22 Pdbmat> Matrix trace = 5.662982E+07 Pdbmat> Larger element = 905.600 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. Diagonalize Tirion matrix using diagrtb Diagrtb> Diagonalizes a matrix, using the RTB/BNM approximation. Diagrtb> Version 2.52, November 2004. Diagrtb> Options to be read in diagrtb.dat file. Diagrtb> Options taken into account: MATRix filename = pdbmat.sdijb COORdinates filename = 22062011140762491.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 1000 Origin of MASS values = CONS MATRix FORMat = BINA Temporary files cleaning = ALL Output PRINting level = 2 Diagrtb> Memory allocation for Blocpdb. Blocpdb> Entering in. Openam> file on opening on unit 10: diagrtb_work.xyzm Blocpdb> Coordinate file 22062011140762491.atom to be opened. Openam> file on opening on unit 11: 22062011140762491.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 34417 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 1000 residue(s) per block. Blocpdb> 2136 residues. Blocpdb> 16290 atoms in block 1 Block first atom: 1 Blocpdb> 15876 atoms in block 2 Block first atom: 16291 Blocpdb> 1699 atoms in block 3 Block first atom: 32167 Blocpdb> 552 atoms in block 4 Block first atom: 33865 Blocpdb> 4 blocks. Blocpdb> At most, 16290 atoms in each of them. Blocpdb> At least, 552 atoms in each of them. Blocpdb> Normal end of Blocpdb. Diagrtb> Memory allocation for Prepmat. Diagrtb> Memory allocation for RTB. Diagrtb> Memory allocation for Diagstd. %Diagrtb-Wn> 24 eigenvectors, only, can be determined. Diagrtb> Memory allocation for RTB_to_modes. %Diagrtb-Er> IIWKMX up to: 481686505 Maximum allowed is LIWORK= 5000000 %Diagrtb-Er> IRWKMX up to: 483552939 Maximum allowed is LRWORK= 32000000 %Diagrtb-Er> Not enough memory allowed for working arrays. Sorry. Lower the number of blocks, the sizes of the largest ones... Or recompile DIAGRTB with larger WORKing arrays. STDERR: STOP *Working arrays allocation error* real 0m0.204s user 0m0.196s sys 0m0.004s




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elNémo is maintained by Yves-Henri Sanejouand.
It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: October 18th, 2018.