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 http://uk.messenger.yahoo.com