[gmx-users] problem with energy minimization

Geraudis Mustelier gera at ict.cim.sld.cu
Wed Dec 12 20:03:46 CET 2001


I would like to refine a model obtained with modeling by homology technique
from X-ray structures. So, I am treating to do an energy minimization. The
parameter values in .mdp file are:
cpp                 =  /lib/cpp
define              = -DPOSRES
constraints       =  none
morse              =  no
integrator         =  steep
nsteps              =  2000
; Energy minimizing stuff
emtol               =  100
emstep             =  0.00001
nstcomm           =  1
ns_type            =  grid
rlist                   =  1
rcoulomb          =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
 But the last results showed in log file are:

Reading file r3md01.tpr, VERSION 3.0.5 (single precision)

Back Off! I just backed up ener.edr to #ener.edr#
   Tolerance         =          100

Stepsize too small Converged to machine precision,
but not to the requested precision (100)
You might need to increase your constraint accuracy

writing lowest energy coordinates.

Back Off! I just backed up r3md01.trr to #r3md01.trr#

Back Off! I just backed up r3md02.pdb to #r3md02.pdb#
Maximum force:  2.14823e+03

STEEPEST DESCENTS did not converge in 82 steps
  Potential Energy  = -2.11852e+05

I have explored with different values for these parameters, but always the
final structure is identical to initial. So, someone can help me to give
correct value to these parameters, or introduce others, in order to obtain
another conformation?
 MSc. Geraudis Mustelier-Portuondo

 Center of Molecular Immunology
 Calle 216 esq. A 15, Atabey, Playa
 A. Postal 16040, Havana 11600, CUBA

 email: gera at ict.cim.sld.cu

 Tel: 53-7-214335
 Fax: 53-7-335049

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