[gmx-users] EM Difficulties.

Joel DeWitt osu_biophysics at hotmail.com
Mon Jul 7 18:39:01 CEST 2003


Greetings gmx-users!  I have come up against a road block that I don't know how to surpass.  Our system is a simple DPPC monolayer consisting of 30 lipid molecules with no water.  I have been using the "S-peptide" section of "Getting Started" as a guide to get my MD up and running.  Now, when I try to energy minimize, I keep getting results that leave the system unchanged:

Steepest Descents:
   Tolerance         =  2.00000e+03
   Number of steps   =          200
Step=    0, Dmax= 1.0e-02 nm, Epot=  7.02686e+04 Fmax= 5.87704e+05, atom= 31
Step=    1, Dmax= 1.0e-02 nm, Epot=  3.51496e+04 Fmax= 1.68366e+05, atom= 31
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.93629e+04 Fmax= 5.30734e+04, atom= 1497
Step=    3, Dmax= 1.4e-02 nm, Epot=  1.14356e+04 Fmax= 1.37348e+04, atom= 31
Step=    4, Dmax= 1.7e-02 nm, Epot=  5.40411e+03 Fmax= 6.98762e+03, atom= 1498
Step=    5, Dmax= 2.1e-02 nm, Epot=  2.42665e+03 Fmax= 4.88417e+03, atom= 1197
Step=    7, Dmax= 1.2e-02 nm, Epot=  1.93304e+03 Fmax= 5.89898e+03, atom= 184
Step=    9, Dmax= 7.5e-03 nm, Epot=  9.61426e+02 Fmax= 3.05110e+03, atom= 184
Step=   11, Dmax= 4.5e-03 nm, Epot=  6.04071e+02 Fmax= 2.58888e+03, atom= 184
Step=   12, Dmax= 5.4e-03 nm, Epot=  4.29385e+02 Fmax= 3.75457e+03, atom= 184
Step=   13, Dmax= 6.4e-03 nm, Epot=  2.63337e+02 Fmax= 4.23455e+03, atom= 184
Step=   14, Dmax= 7.7e-03 nm, Epot=  2.26982e+02 Fmax= 5.06575e+03, atom= 184
Step=   16, Dmax= 4.6e-03 nm, Epot= -3.13108e+02 Fmax= 1.05358e+03, atom= 1231

writing lowest energy coordinates.

Steepest Descents converged to 2000 in 17 steps
  Potential Energy  = -3.13108e+02
Maximum force:  1.05358e+03

I would expect the EM process to run a much longer time; here it only takes a couple of seconds.  Could the simulation be examining only select atoms?  Should the file "em.mdp" be modified to make the minimization process more thorough?  Any help you can provide will be appreciated.

Joel DeWitt
Department of Physics
Oklahoma State University
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