[gmx-users] Vectors in non-cubic box

[afsaneh maleki]

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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