[gmx-users] still problems with dodecahedron box and editconf

[Jochen Hub]

Maybe

trjconv -ur compact 

could help you...

Cheers, Jochen

Sebastian Kruggel wrote:
> Dear gmx-er,
>  
> I have problems creating (or visualizing) a dodecahedron box. I found simular
> problems in the mailing list, where running mdrun is supposed to help - but this does't work in my case.
> I generated my box with the following commands
>  
>   
>> pdb2gmx -f $PROT.pdb -o $PROT.gro -p $PROT.top -ff oplsaa -water spce
>> editconf -bt dodecahedron -f $PROT.gro -o $PROT.ec.pdb -d 0.9
>> genbox -cp $PROT.ec.pdb -cs -o $PROT.b4ion.gro -p $PROT.top
>>     
>  
>   
>> grompp -f $MDP/em.mdp -c $PROT.b4ion.gro -p $PROT.top -o $PROT.b4ion.tpr
>> genion -s $PROT.b4ion.tpr -o $PROT.b4em.gro -nname Cl -nn 1 -g genion.log
>>     
>  
> # and after editing $PROT.top
>  
>   
>> grompp -f $MDP/em.mdp -c $PROT.b4em.gro -p $PROT.top -o em.tpr
>> mdrun -v -s em.tpr -o em.trr -c $PROT.b4pr.gro -e em.edr -g em.log
>>     
>  
> if I look at the tpr/trr with ngmx or chimera, the box is cubic and a very big
> part of the protein is out of the box - I found in the mailing lists that this
> shouldn't be a problem because of the periodic boundary conditions (even if
> the manula says: 'Both -box and -d will center the system in the box').
>  
> I had a look at the tpr-file to see if it's maybe just a problem of
> visualisation. I used gmxdump to look at the topology and found:
>  
>   
>> gmxdump -s pr.tpr | grep box
>>     
>  
> Reading
> file pr.tpr, VERSION 3.2.1 (single precision)
>   
> box (3x3):
>       box[    0]=
> { 8.77170e+00,  0.00000e+00,  0.00000e+00}
>       box[    1]=
> { 0.00000e+00,  8.77170e+00,  0.00000e+00}
>       box[    2]=
> { 4.38585e+00,  4.38585e+00,  6.20253e+00}
>    boxv (3x3):
>       boxv[    0]=
> { 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       boxv[    1]=
> { 0.00000e+00,  0.00000e+00,  0.00000e+00}
>      
> boxv[    2]=
> { 0.00000e+00,  0.00000e+00,  0.00000e+00}
>  
> So the box really looks dodecahedron in the first part, but what about the 0 0
> 0 boxv ?!?
>  
> Maybe somebody can help me figuring out if my box is 'really' dodecahedron?
> Thanks in advance!
>  
> Sebastian
>
>   
> ------------------------------------------------------------------------
>
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************