[gmx-users] More EM Questions.

Joel DeWitt osu_biophysics at hotmail.com
Mon Jul 14 21:57:01 CEST 2003 

gmx-users:

When I run EM on my DPPC monolayer (just 30 lipids), I get peculiar standard 
output:

Steepest Descents:
   Tolerance         =  1.50000e+02
   Number of steps   =         1000
Step=    0, Dmax= 1.0e-01 nm, Epot= -2.81451e+03 Fmax= 6.07879e+02, atom= 
1158
Step=    7, Dmax= 1.6e-03 nm, Epot= -2.82194e+03 Fmax= 1.15606e+03, atom= 
1484
Step=    8, Dmax= 1.9e-03 nm, Epot= -2.86810e+03 Fmax= 1.09084e+03, atom= 
1484
Step=   10, Dmax= 1.1e-03 nm, Epot= -2.88997e+03 Fmax= 2.95926e+02, atom= 
1484
Step=   11, Dmax= 1.4e-03 nm, Epot= -2.89769e+03 Fmax= 1.24415e+03, atom= 
1484
Step=   12, Dmax= 1.6e-03 nm, Epot= -2.91180e+03 Fmax= 7.41073e+02, atom= 
1484
Step=   14, Dmax= 9.7e-04 nm, Epot= -2.91991e+03 Fmax= 4.15367e+02, atom= 
1484
Step=   15, Dmax= 1.2e-03 nm, Epot= -2.92385e+03 Fmax= 1.04241e+03, atom= 
1484
Step=   16, Dmax= 1.4e-03 nm, Epot= -2.93441e+03 Fmax= 6.31874e+02, atom= 
1484
Step=   18, Dmax= 8.4e-04 nm, Epot= -2.94171e+03 Fmax= 4.08596e+02, atom= 
1484
Step=   19, Dmax= 1.0e-03 nm, Epot= -2.94694e+03 Fmax= 7.71140e+02, atom= 
1484
Step=   20, Dmax= 1.2e-03 nm, Epot= -2.95373e+03 Fmax= 7.19116e+02, atom= 
1484
Step=   21, Dmax= 1.5e-03 nm, Epot= -2.95601e+03 Fmax= 1.00670e+03, atom= 
1484
Step=   22, Dmax= 1.7e-03 nm, Epot= -2.96010e+03 Fmax= 1.13041e+03, atom= 
1484
Step=   24, Dmax= 1.0e-03 nm, Epot= -2.97515e+03 Fmax= 1.69570e+02, atom= 
1485
Step=   25, Dmax= 1.3e-03 nm, Epot= -2.98926e+03 Fmax= 1.07089e+03, atom= 
1484
Step=   26, Dmax= 1.5e-03 nm, Epot= -2.99995e+03 Fmax= 7.62335e+02, atom= 
165
Step=   28, Dmax= 9.0e-04 nm, Epot= -3.00881e+03 Fmax= 3.37067e+02, atom= 
1484
Step=   29, Dmax= 1.1e-03 nm, Epot= -3.01011e+03 Fmax= 9.90327e+02, atom= 
165
Step=   30, Dmax= 1.3e-03 nm, Epot= -3.02088e+03 Fmax= 5.66692e+02, atom= 
165
Step=   32, Dmax= 7.8e-04 nm, Epot= -3.02726e+03 Fmax= 4.19713e+02, atom= 
165
Step=   33, Dmax= 9.4e-04 nm, Epot= -3.03087e+03 Fmax= 6.68336e+02, atom= 
165
Step=   34, Dmax= 1.1e-03 nm, Epot= -3.03551e+03 Fmax= 7.43691e+02, atom= 
165
Step=   35, Dmax= 1.3e-03 nm, Epot= -3.03831e+03 Fmax= 8.58881e+02, atom= 
165
Step=   36, Dmax= 1.6e-03 nm, Epot= -3.03840e+03 Fmax= 1.16132e+03, atom= 
165
Step=   37, Dmax= 1.9e-03 nm, Epot= -3.04224e+03 Fmax= 1.16956e+03, atom= 
165
Step=   39, Dmax= 1.2e-03 nm, Epot= -3.05915e+03 Fmax= 2.76643e+02, atom= 
165
Step=   41, Dmax= 7.0e-04 nm, Epot= -3.06420e+03 Fmax= 5.15477e+02, atom= 
165
Step=   42, Dmax= 8.4e-04 nm, Epot= -3.06887e+03 Fmax= 5.45993e+02, atom= 
165
Step=   43, Dmax= 1.0e-03 nm, Epot= -3.07246e+03 Fmax= 6.39860e+02, atom= 
165
Step=   44, Dmax= 1.2e-03 nm, Epot= -3.07461e+03 Fmax= 8.77551e+02, atom= 
165
Step=   45, Dmax= 1.4e-03 nm, Epot= -3.07883e+03 Fmax= 8.54035e+02, atom= 
165
Step=   47, Dmax= 8.7e-04 nm, Epot= -3.08872e+03 Fmax= 2.32541e+02, atom= 
1465
Step=   48, Dmax= 1.0e-03 nm, Epot= -3.09229e+03 Fmax= 9.27919e+02, atom= 
165
Step=   49, Dmax= 1.3e-03 nm, Epot= -3.10090e+03 Fmax= 6.31078e+02, atom= 
165
Step=   51, Dmax= 7.5e-04 nm, Epot= -3.10699e+03 Fmax= 2.61160e+02, atom= 
165
Step=   52, Dmax= 9.0e-04 nm, Epot= -3.10877e+03 Fmax= 9.11788e+02, atom= 
165
Step=   53, Dmax= 1.1e-03 nm, Epot= -3.11789e+03 Fmax= 3.83839e+02, atom= 
165
Step=   55, Dmax= 6.5e-04 nm, Epot= -3.12190e+03 Fmax= 4.45412e+02, atom= 
165
Step=   56, Dmax= 7.8e-04 nm, Epot= -3.12567e+03 Fmax= 4.67017e+02, atom= 
165
Step=   57, Dmax= 9.3e-04 nm, Epot= -3.12822e+03 Fmax= 7.16988e+02, atom= 
165
Step=   58, Dmax= 1.1e-03 nm, Epot= -3.13275e+03 Fmax= 6.18419e+02, atom= 
165
Step=   60, Dmax= 6.7e-04 nm, Epot= -3.13877e+03 Fmax= 2.32835e+02, atom= 
1315
Step=   61, Dmax= 8.1e-04 nm, Epot= -3.14292e+03 Fmax= 6.56500e+02, atom= 
165
Step=   62, Dmax= 9.7e-04 nm, Epot= -3.14788e+03 Fmax= 5.60505e+02, atom= 
1315
Step=   63, Dmax= 1.2e-03 nm, Epot= -3.14889e+03 Fmax= 8.10126e+02, atom= 
165
Step=   64, Dmax= 1.4e-03 nm, Epot= -3.15142e+03 Fmax= 9.32049e+02, atom= 
1315
Step=   65, Dmax= 1.7e-03 nm, Epot= -3.15220e+03 Fmax= 1.07081e+03, atom= 
165
Step=   67, Dmax= 1.0e-03 nm, Epot= -3.16510e+03 Fmax= 1.85081e+02, atom= 
1315
Step=   68, Dmax= 1.2e-03 nm, Epot= -3.17040e+03 Fmax= 1.07637e+03, atom= 
1315
Step=   69, Dmax= 1.4e-03 nm, Epot= -3.17979e+03 Fmax= 7.31210e+02, atom= 
1315
Step=   71, Dmax= 8.7e-04 nm, Epot= -3.18591e+03 Fmax= 2.98363e+02, atom= 
1655
Step=   73, Dmax= 5.2e-04 nm, Epot= -3.18935e+03 Fmax= 3.85888e+02, atom= 
1315
Step=   74, Dmax= 6.2e-04 nm, Epot= -3.19264e+03 Fmax= 3.30996e+02, atom= 
165
Step=   75, Dmax= 7.5e-04 nm, Epot= -3.19549e+03 Fmax= 6.49261e+02, atom= 
1315
Step=   76, Dmax= 9.0e-04 nm, Epot= -3.20007e+03 Fmax= 4.11079e+02, atom= 
1315
Step=   78, Dmax= 5.4e-04 nm, Epot= -3.20389e+03 Fmax= 2.87135e+02, atom= 
1315
Step=   79, Dmax= 6.5e-04 nm, Epot= -3.20709e+03 Fmax= 4.38177e+02, atom= 
1315
Step=   80, Dmax= 7.8e-04 nm, Epot= -3.20989e+03 Fmax= 5.62238e+02, atom= 
1315
Step=   81, Dmax= 9.3e-04 nm, Epot= -3.21299e+03 Fmax= 5.30648e+02, atom= 
1315
Step=   82, Dmax= 1.1e-03 nm, Epot= -3.21319e+03 Fmax= 8.96647e+02, atom= 
1315
Step=   83, Dmax= 1.3e-03 nm, Epot= -3.21801e+03 Fmax= 7.02900e+02, atom= 
1315
Step=   85, Dmax= 8.1e-04 nm, Epot= -3.22402e+03 Fmax= 3.14951e+02, atom= 
1315
Step=   86, Dmax= 9.7e-04 nm, Epot= -3.22506e+03 Fmax= 7.77787e+02, atom= 
1315
Step=   87, Dmax= 1.2e-03 nm, Epot= -3.22953e+03 Fmax= 6.82109e+02, atom= 
1315
Step=   89, Dmax= 7.0e-04 nm, Epot= -3.23481e+03 Fmax= 1.43325e+02, atom= 
1465

writing lowest energy coordinates.

Back Off! I just backed up em.trr to ./#em.trr.1#

Steepest Descents converged to 150 in 90 steps
  Potential Energy  = -3.23481e+03
Maximum force:  1.43325e+02

I've written EM algorithms from scratch before and GROMACS obviously is not 
being thorough in its energy minimization.  Sure, the potential energy is 
being reduced overall, but it doesn't seem like EM is examining the system 
as a whole; just a handful of atoms.

Do I need to write a script that will do many EM runs in a row so that I can 
get this system ready for some MD?

One other thing I've been thinking about: some people have donated sets of 
force field parameters to GROMACS.org:

ffG43a2x.tgz (GROMOS96 modified to describe lipids)
ffgmx_lipids.tar.gz (lipid params for use with ffgmx)

Is this part of my EM problem?  Do I need these?

Joel DeWitt
Department of Physics
Oklahoma State University

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