[gmx-users] substrate explodes

YOLANDA SMALL yas102 at psu.edu
Tue Sep 21 18:28:48 CEST 2004

Hello gmx-users,

I did an energy minimization on a protein system for which I constructed a
topology file for the unique substrate and cofactor at the active site.  I used
the freezegrp option to freeze the substrate and cofactor in all directions (my
.mdp file is below).  The energy minization does not converge but delivers this

Stepsize too small (7.49853e-07 nm)Converged to machine precision,
but not to the requested precision (1000)

Steepest Descents did not converge in 75 steps
  Potential Energy  =  3.08892e+08
Maximum force:  1.99058e+06

Upon inspection of the output structure, the substrate and cofactor are the only
things that have exploded even though I thought that freezing them keeps them
fixed.  Does anyone know what could be causing this problem?

mdp filecpp                 =  /lib/cpp
define              =  -DFLEX_SPC
; constraints         =  all-bonds
integrator          =  steep
nsteps              =  300
;       Energy minimizing stuff
emtol               =  1000
emstep              =  0.0001

nstcomm             =  1
ns_type             =  grid
pbc                 =  xyz
rlist               =  1
coulombtype         =  cut-off
rcoulomb            =  1.4
vdwtype             =  cut-off
rvdw                =  1.4
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
;      Frozen Groups
freezegrps          =  ORO FMN
freezedim           =  Y Y Y Y Y Y

Many thanks,

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