[gmx-users] basic question about code

[Luciano]

 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?!  
 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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