Log file opened on Wed Aug 26 16:44:18 2009 Host: pople4700.psc.teragrid.org pid: 3554071 nodeid: 3 nnodes: 4 The Gromacs distribution was built Wed Sep 24 22:56:05 EDT 2008 by blood@pople4700.psc.teragrid.org (Linux 2.6.16.46-0.12-default ia64) Max number of connections per atom is 2 Total number of connections is 532 Max number of graph edges per atom is 2 Total number of graph edges is 532 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 1.000 Removing pbc first time Done rmpbc Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 10321.3 There are: 399 Atoms Constraining the starting coordinates (step -2) ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Going to use C-settle (133 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074 rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Started mdrun on node 3 Wed Aug 26 16:44:18 2009 Grid: 4 x 6 x 4 cells Configuring nonbonded kernels... Testing ia64 CPU family...Unknown Itanium You might want to test the speed without assembly kernels by setting the NOASSEMBLYLOOPS environment variable. Using single precision ia64 assembly kernels. Total NODE time on node 3: 0.968 Average NODE time: 0.727 Load imbalance reduced performance to 133% of max LJ 337256. Buckingham 0. VdW(T) 0. Coulomb 29057917. Coulomb [W3] 0. Coulomb [W3-W3] 0. Coulomb [W4] 0. Coulomb [W4-W4] 0. Coulomb + LJ 3983384. Coulomb + LJ [W3] 0. Coulomb + LJ [W3-W3] 0. Coulomb + LJ [W4] 0. Coulomb + LJ [W4-W4] 0. Coulomb + Bham 0. Coulomb + Bham [W3] 0. Coulomb + Bham [W3-W3] 0. Coulomb + Bham [W4] 0. Coulomb + Bham [W4-W4] 0. Coulomb + VdW(T) 0. Coulomb + VdW(T) [W3] 0. Coulomb + VdW(T) [W3-W3] 0. Coulomb + VdW(T) [W4] 0. Coulomb + VdW(T) [W4-W4] 0. RF Coul 0. RF Coul [W3] 0. RF Coul [W3-W3] 0. RF Coul [W4] 0. RF Coul [W4-W4] 0. RF Coul + LJ 0. RF Coul + LJ [W3] 0. RF Coul + LJ [W3-W3] 0. RF Coul + LJ [W4] 0. RF Coul + LJ [W4-W4] 0. RF Coul + Bham 0. RF Coul + Bham [W3] 0. RF Coul + Bham [W3-W3] 0. RF Coul + Bham [W4] 0. RF Coul + Bham [W4-W4] 0. RF Coul + VdW(T) 0. RF Coul + VdW(T) [W3] 0. RF Coul + VdW(T) [W3-W3] 0. RF Coul + VdW(T) [W4] 0. RF Coul + VdW(T) [W4-W4] 0. Coul(T) 0. Coul(T) [W3] 0. Coul(T) [W3-W3] 0. Coul(T) [W4] 0. Coul(T) [W4-W4] 0. Coul(T) + LJ 0. Coul(T) + LJ [W3] 0. Coul(T) + LJ [W3-W3] 0. Coul(T) + LJ [W4] 0. Coul(T) + LJ [W4-W4] 0. Coul(T) + Bham 0. Coul(T) + Bham [W3] 0. Coul(T) + Bham [W3-W3] 0. Coul(T) + Bham [W4] 0. Coul(T) + Bham [W4-W4] 0. Coul(T) + VdW(T) 0. Coul(T) + VdW(T) [W3] 0. Coul(T) + VdW(T) [W3-W3] 0. Coul(T) + VdW(T) [W4] 0. Coul(T) + VdW(T) [W4-W4] 0. Generalized Born Coulomb 0. GB Coulomb + LJ 0. GB Coulomb + VdW(T) 0. LJ NF 0. Buckingham NF 0. VdW(T) NF 0. Coulomb NF 0. Coulomb [W3] NF 0. Coulomb [W3-W3] NF 0. Coulomb [W4] NF 0. Coulomb [W4-W4] NF 0. Coulomb + LJ NF 0. Coulomb + LJ [W3] NF 0. Coulomb + LJ [W3-W3] NF 0. Coulomb + LJ [W4] NF 0. Coulomb + LJ [W4-W4] NF 0. Coulomb + Bham NF 0. Coulomb + Bham [W3] NF 0. Coulomb + Bham [W3-W3] NF 0. Coulomb + Bham [W4] NF 0. Coulomb + Bham [W4-W4] NF 0. Coulomb + VdW(T) NF 0. Coulomb + VdW(T) [W3] NF 0. Coulomb + VdW(T) [W3-W3] NF 0. Coulomb + VdW(T) [W4] NF 0. Coulomb + VdW(T) [W4-W4] NF 0. RF Coul NF 0. RF Coul [W3] NF 0. RF Coul [W3-W3] NF 0. RF Coul [W4] NF 0. RF Coul [W4-W4] NF 0. RF Coul + LJ NF 0. RF Coul + LJ [W3] NF 0. RF Coul + LJ [W3-W3] NF 0. RF Coul + LJ [W4] NF 0. RF Coul + LJ [W4-W4] NF 0. RF Coul + Bham NF 0. RF Coul + Bham [W3] NF 0. RF Coul + Bham [W3-W3] NF 0. RF Coul + Bham [W4] NF 0. RF Coul + Bham [W4-W4] NF 0. RF Coul + VdW(T) NF 0. RF Coul + VdW(T) [W3] NF 0. RF Coul + VdW(T) [W3-W3] NF 0. RF Coul + VdW(T) [W4] NF 0. RF Coul + VdW(T) [W4-W4] NF 0. Coul(T) NF 0. Coul(T) [W3] NF 0. Coul(T) [W3-W3] NF 0. Coul(T) [W4] NF 0. Coul(T) [W4-W4] NF 0. Coul(T) + LJ NF 0. Coul(T) + LJ [W3] NF 0. Coul(T) + LJ [W3-W3] NF 0. Coul(T) + LJ [W4] NF 0. Coul(T) + LJ [W4-W4] NF 0. Coul(T) + Bham NF 0. Coul(T) + Bham [W3] NF 0. Coul(T) + Bham [W3-W3] NF 0. Coul(T) + Bham [W4] NF 0. Coul(T) + Bham [W4-W4] NF 0. Coul(T) + VdW(T) NF 0. Coul(T) + VdW(T) [W3] NF 0. Coul(T) + VdW(T) [W3-W3] NF 0. Coul(T) + VdW(T) [W4] NF 0. Coul(T) + VdW(T) [W4-W4] NF 0. Generalized Born Coulomb NF 0. GB Coulomb + LJ NF 0. GB Coulomb + VdW(T) NF 0. Free energy innerloop 0. Outer nonbonded loop -9771099018. 1,4 nonbonded interactions 0. Calc Weights 0. Spread Q 0. Spread Q Bspline 0. Gather F 0. Gather F Bspline 0. 3D-FFT 0. Convolution 0. Solve PME 0. NS-Pairs 1183392. Reset In Box 20349. Shift-X 399798. CG-CoM 6783. Sum Forces 602202. Bonds 0. G96Bonds 0. FENE Bonds 0. Angles 0. G96Angles 0. Quartic Angles 0. Propers 0. Impropers 0. RB-Dihedrals 0. Four. Dihedrals 0. Dist. Restr. 0. Orient. Restr. 0. Dihedral Restr. 0. Pos. Restr. 0. Angle Restr. 0. Angle Restr. Z 0. Morse Potent. 0. Cubic Bonds 0. Water Pol. 0. Thole Pol. 0. Virial 222444. Update 199899. Ext.ens. Update 0. Stop-CM 199500. P-Coupling 0. Calc-Ekin 200298. Lincs 0. Lincs-Mat 0. Shake 0. Constraint-V 199899. Shake-Init 0. Constraint-Vir 200697. Settle 66899. Virtual Site 2 0. Virtual Site 3 0. Virtual Site 3fd 0. Virtual Site 3fad 0. Virtual Site 3out 0. Virtual Site 4fd 0. Finished mdrun on node 3 Wed Aug 26 16:44:19 2009