[gmx-users] problem with genbox

[Ashish Gupta]

Dear gmx-users,
   
    I am new to gromacs. While inserting water molecules in an empty 
box, I give the following
command
genbox -ci w.gro -nmol 2400 -box 4 4 4 -o only_water.gro

where w.gro contains

216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
 3
    1SOL     OW    1    .230    .628    .113
    1SOL    HW1    2    .137    .626    .150
    1SOL    HW2    3    .231    .589    .021
  0.31 0.31  0.31

The resulting output contains atoms which are too close. The distance 
between the atoms is sometimes
as small as 0.01 nm which is smaller than the vanderwaals radii from the 
database vdwradii.dat . Not
surprisingly, therefore I get errors when I run energy minimization or 
mdrun.
  The output keeps repeating the message "tested 0 pairs,  removed 0 
atoms " as I quote below.  I would
greatly appreciate if somebody could guide me how to use genbox properly.

Thanks,
Ashish Gupta.

The output of genbox is ...
"
Opening library file /home/gromacs/share/top/aminoacids.dat
Opening library file /home/gromacs/share/top/atommass.dat
Opening library file /home/gromacs/share/top/vdwradii.dat
Opening library file /home/gromacs/share/top/dgsolv.dat
Reading molecule configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 0box_margin = 0.315
Removed 0 atoms that were outside the box
nri = 3, nrj = 3
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
 success (now 3 atoms)!Try 1box_margin = 0.315
Removed 0 atoms that were outside the box
nri = 3, nrj = 3
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
 success (now 6 atoms)!Try 2box_margin = 0.315
Removed 0 atoms that were outside the box
nri = 3, nrj = 3
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
 success (now 9 atoms)!Try 3box_margin = 0.315
Removed 0 atoms that were outside the box
nri = 3, nrj = 3
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
 success (now 12 atoms)!Try 4box_margin = 0.315
Removed 0 atoms that were outside the box
nri = 3, nrj = 3
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
 success (now 15 atoms)!Try 5box_margin = 0.315
Removed 0 atoms that were outside the box
 genbox contains -
"    Similar message keeps repeating.