[gmx-users] size of the system

[V.V. Chaban]

It seems my answer to Berk was processes by the system
in a wrong way.

>  guess this procedure should work, so this might be a bug.
> But you are making things much more complicated than needed.
> You can skip the first two steps and just use the -box option of genbox instead of -cp.
> 
> Berk.

OK. 
genbox -cs spc216.pdb -box 3 3 3.
It outputs:
      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
        -box vector  3 3 3  box size
       -nmol    int      0  no of extra molecules to insert
        -try    int     10  try inserting -nmol*-try times
       -seed    int   1997  random generator seed
       -vdwd   real  0.105  default vdwaals distance
      -shell   real      0  thickness of optional water layer around solute
     -maxsol    int      0  maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is
                            ignored

WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solvent configuration
""
solvent configuration contains 648 atoms in 216 residues

And hangs up. 
:(
>



OK. 
genbox -cs spc216.pdb -box 3 3 3.
It outputs:
      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
        -box vector  3 3 3  box size
       -nmol    int      0  no of extra molecules to insert
        -try    int     10  try inserting -nmol*-try times
       -seed    int   1997  random generator seed
       -vdwd   real  0.105  default vdwaals distance
      -shell   real      0  thickness of optional water layer around solute
     -maxsol    int      0  maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is
                            ignored

WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solvent configuration
""
solvent configuration contains 648 atoms in 216 residues

And hangs up. 
What can it be?

Vitaly