[gmx-users] results of energy minimization

[Justin A. Lemkul]

Quoting s lal badshah <shahbiochemist at yahoo.com>:

> Dear gromacs experts,
> I have run the energy minimization of a protein.With the tail command it
> shows the following results:
> ahmad at uop:~/protein> tail -15 md.log
>  NS-Pairs                         94.365846     1981.682766    20.0
>  Reset In Box                      0.569385        5.124465     0.1
>  Shift-X                           0.569310        3.415860     0.0
>  CG-CoM                            0.190785        5.532765     0.1
>  Bonds                             0.394530       16.964790     0.2
>  Angles                            0.253320       41.291160     0.4
>  Propers                           0.009855        2.256795     0.0
>  RB-Dihedrals                      0.086835       21.448245     0.2
> -----------------------------------------------------------------------
>  Total                                          9893.632954   100.0
> -----------------------------------------------------------------------
>
>                NODE (s)   Real (s)      (%)
>        Time:     15.000     15.000    100.0
> Finished mdrun on node 0 Wed Mar 12 12:50:59 2008
> I have check the em.log file, which shows the following data:
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.9742134e+21
> Maximum force     =  4.1648520e+06 on atom 1934
> Norm of force     =  5.6557945e+06
> 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 command

EM is finished, hence the line in your md.log file that tells you "Finished
mdrun..."  Using the top command, you will undoubtedly see lots of things
fluctuating, as there are (hopefully) several processes on your machine that
are keeping it working.  What you are looking for is "mdrun," which, as I said,
should have finished.

You will also note that mdrun is telling you that it "converged to machine
precision," which means the algorithm has reached a satisfactory end, within
the limits of your hardware.

-Justin

> 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.
> Regards,
> Lal badshah.
>
>  Send instant messages to your online friends http://uk.messenger.yahoo.com



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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