[gmx-users] genconf, grompp

[Mark Abraham]

On 11/03/2012 2:50 PM, saly jackson wrote:
>
>
> 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?

You've been given all the help you can be given with the information 
you're giving us. See 
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069235.html.

Mark