[gmx-users] basic question about code

[David]

On Tue, 2003-11-11 at 20:46, Luciano wrote:
>   Hi gmx-users,
> 
>  How described by Nuno, I have started my EM and MD protocol with the
> system composed of protein + water.
> 
>  I tried, inicially, to minimize the system with:
> 
> emtol                   = 50
> emstep                  = 0.01
> nstcgsteep              = 5
> cpp                     = /lib/cpp
> ;define                  =  -DPOSRES
> define                  =  -DFLEX_SPC
> integrator              = cg              ; after steep 
> nsteps                  = 5000
> nstcomm                 =  1                     
> nstlog                  = 100
> nstlog                  = 100
> nstenergy               = 100
> nstlist                 = 10
> ns_type                 = grid
> tcoupl                  = no
> pcoupl                  = no
> constraints             = none
> rlist                   = 1.0
> rcoulomb                = 1.0
> rvdw                    = 1.0
> 
>  Well, without PR and cg method the mdrun generate:
> 
>  "error : ci reason; f = high number " (check nsgrid.c ...)" 
> 
>  Then, I think it would be due to no existence of PR, futher high nember
> f, changing to define = -DPOSRE and steep.
> 
>  Run the grompp and mdrun and nothing error was showed. But, after steps
> the EM shows:
> 
> 
>  "Stepsize too small (5.8413e-07 nm)Converged to machine precision,
> but not to the requested precision (50)
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> Steepest Descents did not converge in 663 steps
>   Potential Energy  =  1.05729e+06
> Maximum force:  3.07947e+04"
> 
>  Have I to change for a double precision?!  


if you have positive energies for a system containing water then your
starting structure is wrong someway (or maybe the box)

>  Is there anybody to help me?!
> 
>  Thanks in advance...
> 
>  Luciano
>  
> 
> 
> ######################################################
>                Luciano Tavares da Costa
>              Mestre em Engenharia Química
>    icq #232852036 ; ltcosta at universiabrasil.net  
>     Doutorando Laboratório de Biofisicoquímica
>               Instituto de Química - USP
>              
> ######################################################
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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