[gmx-users] editconf and genbox using method

[Nuno Azoia]

Hello!

Your box isn't rectangular. Your problem is just VMD display the gro
file with a rectangular shape. If you need to see your system properly
try to transform your .gro file in a .pdb file first, using trjconv.

Try trjconv -h to see the options

Nuno Azoia

On Mon, 2009-03-09 at 12:23 +0200, Marian Butu wrote:
> Hi,
> 
> I want to obtain a dodecahedron box to start a simulation of a small
> peptide. But, even if I use dodecahedron option or octahedron, I
> obtain a rectangular box.
> 
>  
> 
> Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after
> 3.2.1 binaries for MS Windows)
> 
> Command line that I used:
> 
>   pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p
> 
>   editconf -f pep1 -o -bt octahedron -d 0.3 -c
> 
>   genbox -cp out -cs -p pep1 -o pep1_em
> 
>  
> 
> And, when I'm looking to pep1_em.gro with VMD the box is very very
> rectangular.
> 
>  
> 
> Please, somebody help me with this problem.
> 
>  
> 
> PS. I'm a new user of Gromacs but I'm read all the messages from the
> www.mail-archive.com/gmx-users at gromacs.org about this problem but I
> still don't understand what I need to do to obtain the correct box.
> 
>  
> 
> Thank you very much in advance for any suggestion.
> 
> Marian
> 
> 
>  
>  
>  
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