Log file opened on Wed Aug 26 16:41:03 2009 Host: pople4700.psc.teragrid.org pid: 3506712 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 Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 1604 Started Steepest Descents on node 3 Wed Aug 26 16:41:03 2009 ++++ 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 --- -------- -------- Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 100 Going to use C-settle (133 waters) wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897 rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 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. Finished mdrun on node 3 Wed Aug 26 16:41:04 2009