[gmx-users] Vectors in non-cubic box

[Tsjerk Wassenaar]

Hi Afsaneh,

The PBC and the .gro file format are explained in the manual, chapter 3.
The last line of the .gro file has the box stored as

XX YY ZZ XY XZ YX YZ ZX ZY

Cheers,

Tsjerk

On Mar 5, 2011 6:03 AM, "afsaneh maleki" <maleki.afsaneh at gmail.com> wrote:

Hi,

I want to create  *.gro file with simulation box size as following:

 3.4604674520000      0.000000000000      0.000000000000

 1.7302337260000     2.9968527222000      0.000000000000

 0.000000000000       0.000000000000      10.0000000000

I used the command:

]editconf     –f  *.pdb   –o *.gro   –box  3.46   3.46   10.    –c    –angle
 90  90  60

 are these commands  proper to create this simulation box size?



 system size :  4.975  2.951  0.084 (nm)

    center      :  0.025  0.548  0.966 (nm)

    box vectors :  0.000  0.000  0.000 (nm)

    box angles  :   0.00   0.00   0.00 (degrees)

    box volume  :   0.00               (nm^3)

    shift       :  2.570  0.951  4.034 (nm)

new center      :  2.595  1.498  5.000 (nm)

new box vectors :  3.460  3.460 10.000 (nm)

new box angles  :  90.00  90.00  60.00 (degrees)

new box volume  : 103.68               (nm^3)



Also I paste some .gro file

    1       NAU   39   1.759   1.647   4.998

    1       HAC   41   1.855   1.618   4.993

    1       HAB   40   1.686   1.578   5.002

   3.46000   2.99645   10.00000   0.00000   0.00000   1.73000   0.0000
-0.0000   -0.00000



What is three last values in box vector,0.00 -0.00 -.0 0?


Would one please clear me about these vectors?



3.46000   2.99645   10.00000   0.00000   0.00000   1.73000   0.0000
-0.0000   -0.00000

xx           yy                 zz                 ?             ?
xy          ?            ?             ?


I have another question that does  g_hbond has the compatibility with
non-cubic (or parallelpiped) cells?


good luck
Afsaneh


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