Single CPU run. These are the last lines of the log file:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 0.000 Generated table with 1000 data points for Ewald. Tabscale = 500 points/nm Generated table with 1000 data points for LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for LJ12. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm 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. Removing pbc first time Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- The number of constraints is 1142 ++++ 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 --- -------- -------- Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ 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 --- -------- -------- 2008/10/26 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >> Hello! >> I'm using gromacs 4.0 on an sgi server. Everything compiled OK. Every >> program in gromacs runs OK, except mdrun. Mdrun stops every time at this >> point: >> Loaded with Money >> starting mdrun 'IMMUNOGLOBULIN G BINDING PROTEIN G in water' >> 100000 steps, 200.0 ps. >> >> Then nothing happens.The CPU usage is 0%, and the .trr and .xtc files >> remain 0 bytes. What is the problem? >> > > What does the log file say? Are you running in parallel? If so, how? Do > other parallel codes work? > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sun Li Department of Physics Nanjing University, China
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
