[gmx-users] editconf/genbox: molecular complex outside simulation box

[vedat durmaz]

thanks. things are getting clearer and life's going a little easier, now.


Justin A. Lemkul schrieb:
>
>
> durmaz at zib.de wrote:
>> hi there,
>>
>> it's my first steps with gromacs and i can't get rid of the following
>> problem:
>>
>> i set up my box with
>>
>> editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9
>>
>> and fill it up with water like
>>
>> genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p
>> complex.top
>>
>> but when viewing the system of the resulting file (outfile.pdb),
>> parts of
>> the molecular complex turn out to be outside the box, although the
>> box is
>> obviously large enough. the complex is not centered, whether i use -c or
>> not. i've tried several water models (tip4p, ffamber_tip3p) and all box
>> shapes such as an octahedron, dodecah., cube, triclinic. the cubic
>> one is
>> the only one to result in a properly centered complex. but i prefer
>> to use
>> other box types.
>>
>> does anyone have an idea of the stage at which to search the cause for
>> that problem?
>>
>> thanks a lot and regards
>
> This is just a visualization artifact.  See, for instance:
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
> You can "correct" it by using trjconv (once you have assembled a .tpr
> file):
>
> trjconv -s *.tpr -f outfile.pdb -pbc mol -ur compact
>
> -Justin
>