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
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