[gmx-users] substrate explodes

[David]

On Tue, 2004-09-21 at 18:28, YOLANDA SMALL wrote:
> 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
> message: 
> 
> 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
Freezing is not compatible with energy minimization. Considering the
huge forces you have a bad structure or bad topology.
> 
> 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,
> Yolanda
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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