Hello!
Check out
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
Cheers
/Per
12 mar 2008 kl. 11.58 skrev s lal badshah:
Dear gromacs experts,
I have run the energy minimization of a protein.With the tail
command it shows the following results:
[EMAIL PROTECTED]:~/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 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.
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