[gmx-users] genconf, grompp

[saly jackson]

Hi all

When we want to fill a box containing for example 60000 molecules we can
not use genbox. We have to use genconf to build it.

 genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro

When I use this command as I want a box including 60000 molecules are
filled When I open .gro file of the filled box I see the following format:


Great Red Owns Many ACres of Sand
60000
   1DRG    CAA    1   0.495  -0.175  -0.072  0.0000  0.0000  0.0000
   1DRG    CAB    2   0.483  -0.311  -0.143  0.0000  0.0000  0.0000
   1DRG    CAC    3   0.388  -0.406  -0.069  0.0000  0.0000  0.0000
   1DRG    CAD    4   0.451  -0.463   0.058  0.0000  0.0000  0.0000
   1DRG    CAE    5   0.352  -0.557   0.127  0.0000  0.0000  0.0000
   1DRG    CAF    6   0.415  -0.613   0.255  0.0000  0.0000  0.0000
   2DRG    CAA    7   0.495  -0.175  -0.072  0.0000  0.0000  0.0000
   2DRG    CAB    8   0.483  -0.311  -0.143  0.0000  0.0000  0.0000
   2DRG    CAC    9   0.388  -0.406  -0.069  0.0000  0.0000  0.0000
   2DRG    CAD   10   0.451  -0.463   0.058  0.0000  0.0000  0.0000
   2DRG    CAE   11   0.352  -0.557   0.127  0.0000  0.0000  0.0000
   2DRG    CAF   12   0.415  -0.613   0.255  0.0000  0.0000  0.0000
   3DRG    CAA   13   0.495  -0.175  -0.072  0.0000  0.0000  0.0000
   3DRG    CAB   14   0.483  -0.311  -0.143  0.0000  0.0000  0.0000

But when I want to minimise the simulation box and use grompp as the
following:


grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1


I receive the following error:



------------------------------
-------------------------
Program grompp, VERSION 4.5.4
Source code file: grompp.c, line: 1370

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



Would you please help me?

Thanks

Saly
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