<br><div class="gmail_quote"><br>Hi all<br><br>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. <br><br> genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro<br>
<br>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:<br><br>
<br>
Great Red Owns Many ACres of Sand<br>
60000<br>
1DRG CAA 1 0.495 -0.175 -0.072 0.0000 0.0000 0.0000<br>
1DRG CAB 2 0.483 -0.311 -0.143 0.0000 0.0000 0.0000<br>
1DRG CAC 3 0.388 -0.406 -0.069 0.0000 0.0000 0.0000<br>
1DRG CAD 4 0.451 -0.463 0.058 0.0000 0.0000 0.0000<br>
1DRG CAE 5 0.352 -0.557 0.127 0.0000 0.0000 0.0000<br>
1DRG CAF 6 0.415 -0.613 0.255 0.0000 0.0000 0.0000<br>
2DRG CAA 7 0.495 -0.175 -0.072 0.0000 0.0000 0.0000<br>
2DRG CAB 8 0.483 -0.311 -0.143 0.0000 0.0000 0.0000<br>
2DRG CAC 9 0.388 -0.406 -0.069 0.0000 0.0000 0.0000<br>
2DRG CAD 10 0.451 -0.463 0.058 0.0000 0.0000 0.0000<br>
2DRG CAE 11 0.352 -0.557 0.127 0.0000 0.0000 0.0000<br>
2DRG CAF 12 0.415 -0.613 0.255 0.0000 0.0000 0.0000<br>
3DRG CAA 13 0.495 -0.175 -0.072 0.0000 0.0000 0.0000<br>
3DRG CAB 14 0.483 -0.311 -0.143 0.0000 0.0000 0.0000<br>
<br>
But when I want to minimise the simulation box and use grompp as the following:<br><br><br>
grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1<br><br><br>I receive the following error:<br><br><br><br>
------------------------------<div id=":12n">-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: grompp.c, line: 1370<br>
<br>
Fatal error:<br>
There was 1 error in input file(s)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div><br><br><br>Would you please help me?<br><br>Thanks<span class="HOEnZb"><font color="#888888"><br>
<br>Saly<br><br><br>
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