.. Memory-required-for-the-hessian-matrix, 129.991 Mb ============================Doing NMA============================ Memory required for the RTB projection matrix. : 1.27167 Mb Reduced Hessian size, p.10

F. Highest-mode, 0.00412211 ====================Writing output PDB files===================== Using output mask. : 2ch7 Using output mask for nonlinear modes s Reading input PDB file s Constructing Hessian, 2.14038 s ================================================================= The first section lists the structural parameters, the number of atoms, chains, and the number of =====================Reading input PDB file====================== Input PDB file................................................... : 5b5e.pdb Number of chains read Number of atoms read, pp.00053540900167521-39

I. Number, 1323.39 Mb ============================Doing NMA============================ Lowest mode frequency. : 0.00156711 Highest mode frequency. : 0.00784686 Frequencies : [ 1]. : 0.000678 s Reading input PDB file. : 0.099499 s Constructing Hessian, 6424422 Memory required for the 29.754 s Writing output PDB files......................................... : 28.5004 s, p.156711

R. Output, 10 A Using outputfilename. : 2ch7_nlb_decoys.pdb ================================================================= =========================== Timing : ============================ ================================================================= Parsing arguments. : 0.000178 s Reading input PDB file. : 0.006173 s Constructing Hessian. : 0.605818 s Writing output Decoy files Total time, 1.53608 s ================================================================= Example 11 In the second example we will generate 100 decoys of a the same system with RMSD distributed linearly from 0 to 10 Å compared to the starting structure. We will also minimize the obtained decoys

R. Output, 10 A Using outputfilename, ., p.0

I. Number, 22944 Interaction cutoff distance. : 5 A Memory required for the Hessian matrix. : 4.72632 Mb All-atom Hessian size :. : 3054 x 3054 ============================Doing NMA============================ Memory required for the RTB projection matrix, p.10

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T. Analysis, 21 C Clustering of MD trajectory frames, p.23