<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello!<div><br class="webkit-block-placeholder"></div><div>Check out</div><div><a href="http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision">http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision</a></div><div><br class="webkit-block-placeholder"></div><div>Cheers</div><div>/Per</div><div><br class="webkit-block-placeholder"></div><div><br><div><div>12 mar 2008 kl. 11.58 skrev s lal badshah:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear gromacs experts,<br>I have run the energy minimization of a protein.With the tail command it shows the following results:<br>ahmad@uop:~/protein> tail -15 md.log<br> <span style="font-weight: bold;">NS-Pairs 94.365846 1981.682766 20.0</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Reset In Box 0.569385 5.124465 0.1</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Shift-X 0.569310 3.415860 0.0</span><br style="font-weight: bold;"><span style="font-weight: bold;"> CG-CoM 0.190785 5.532765 0.1</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Bonds 0.394530 16.964790 0.2</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Angles 0.253320 41.291160 0.4</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Propers 0.009855 2.256795 0.0</span><br style="font-weight: bold;"><span style="font-weight: bold;"> RB-Dihedrals 0.086835 21.448245 0.2</span><br style="font-weight: bold;"><span style="font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Total 9893.632954 100.0</span><br style="font-weight: bold;"><span style="font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;"> NODE (s) Real (s) (%)</span><br style="font-weight: bold;"><span style="font-weight: bold;"> Time: 15.000 15.000 100.0</span><br style="font-weight: bold;"><span style="font-weight: bold;">Finished mdrun on node 0 Wed Mar 12 12:50:59 2008</span><br>I have check the em.log file, which shows the following data:<br><br><span style="font-weight: bold;">Steepest Descents converged to machine precision in 15 steps,</span><br style="font-weight: bold;"><span style="font-weight: bold;">but did not reach the requested Fmax < 1000.</span><br style="font-weight: bold;"><span style="font-weight: bold;">Potential Energy = -1.9742134e+21</span><br style="font-weight: bold;"><span style="font-weight: bold;">Maximum force = 4.1648520e+06 on atom 1934</span><br style="font-weight: bold;"><span style="font-weight: bold;">Norm of force = 5.6557945e+06</span><br>Is the energy minimization finished or not? when I use the top command the values fluctuates.As there any specific value or notation below the <span style="font-weight: bold;">command </span>name from which I know that energy minimization is running or finished.As in amber software the word sander is written below the command when check with "top ".Here X is written.<br>Regards,<br>Lal badshah.<br><p> Send instant messages to your online friends <a href="http://uk.messenger.yahoo.com">http://uk.messenger.yahoo.com</a> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</p></blockquote></div><br></div></body></html>