<div>Single CPU run. These are the last lines of the log file:</div>
<div> </div>
<div> </div>
<div> </div>
<div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen <br>A smooth particle mesh Ewald method<br>J. Chem. Phys. 103 (1995) pp. 8577-8592<br>
-------- -------- --- Thank You --- -------- --------</div>
<div>Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br>Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br>System total charge: 0.000<br>Generated table with 1000 data points for Ewald.<br>Tabscale = 500 points/nm<br>
Generated table with 1000 data points for LJ6.<br>Tabscale = 500 points/nm<br>Generated table with 1000 data points for LJ12.<br>Tabscale = 500 points/nm<br>Generated table with 1000 data points for 1-4 COUL.<br>Tabscale = 500 points/nm<br>
Generated table with 1000 data points for 1-4 LJ6.<br>Tabscale = 500 points/nm<br>Generated table with 1000 data points for 1-4 LJ12.<br>Tabscale = 500 points/nm<br>Configuring nonbonded kernels...<br>Testing ia64 CPU family...Unknown Itanium<br>
You might want to test the speed without assembly kernels<br>by setting the NOASSEMBLYLOOPS environment variable.<br>Using single precision ia64 assembly kernels.</div>
<div>Removing pbc first time</div>
<div>Initializing LINear Constraint Solver</div>
<div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>LINCS: A Linear Constraint Solver for molecular simulations<br>J. Comp. Chem. 18 (1997) pp. 1463-1472<br>
-------- -------- --- Thank You --- -------- --------</div>
<div>The number of constraints is 1142</div>
<div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>S. Miyamoto and P. A. Kollman<br>SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid<br>Water Models<br>J. Comp. Chem. 13 (1992) pp. 952-962<br>
-------- -------- --- Thank You --- -------- --------</div>
<div>Center of mass motion removal mode is Linear<br>We have the following groups for center of mass motion removal:<br> 0: rest</div>
<div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak<br>Molecular dynamics with coupling to an external bath<br>J. Chem. Phys. 81 (1984) pp. 3684-3690<br>
-------- -------- --- Thank You --- -------- --------</div>
<div> </div>
<div> </div>
<div><br><br> </div>
<div class="gmail_quote">2008/10/26 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">Lee Soin wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello!<br>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:<br>
Loaded with Money<br>starting mdrun 'IMMUNOGLOBULIN G BINDING PROTEIN G in water'<br>100000 steps, 200.0 ps.<br><br>Then nothing happens.The CPU usage is 0%, and the .trr and .xtc files remain 0 bytes. What is the problem?<br>
</blockquote><br></div>What does the log file say? Are you running in parallel? If so, how? Do other parallel codes work?<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Sun Li<br>Department of Physics<br>Nanjing University, China<br>