[gmx-users] genconf and density of system

Moeed lecielll at googlemail.com
Thu May 13 21:14:03 CEST 2010


Hello,

I intend to generate a stack of molecules with the command line:

genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro

Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules
per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels.
What I get from the above command is (-nbox 8 6 4 )192 but the system size
in getting bigger as well!.  * 24.00000  18.00000  12.00000 nm^3.*

Could you dear experts guide me how I can reach the system density I want.
Also to I wanted to know what is best value -dist option. Is it ok if I
leave the distance between boxes 0 0 0?

Thank you,

Hexane-STACK.gro:

Glycine aRginine prOline Methionine Alanine Cystine Serine
 3840
    1HEX     C1    1   1.786   1.639   1.501  0.0000  0.0000  0.0000
    1HEX    H11    2   1.881   1.608   1.500  0.0000  0.0000  0.0000
    1HEX    H12    3   1.768   1.696   1.421  0.0000  0.0000  0.0000
    1HEX    H13    4   1.770   1.692   1.584  0.0000  0.0000  0.0000
    1HEX     C2    5   1.693   1.518   1.499  0.0000  0.0000  0.0000
    1HEX    H21    6   1.711   1.461   1.579  0.0000  0.0000  0.0000
    1HEX    H22    7   1.710   1.465   1.416  0.0000  0.0000  0.0000
    1HEX     C3    8   1.547   1.561   1.501  0.0000  0.0000  0.0000
    1HEX    H31    9   1.528   1.617   1.420  0.0000  0.0000  0.0000
    1HEX    H32   10   1.530   1.615   1.584  0.0000  0.0000  0.0000
    1HEX     C4   11   1.454   1.440   1.500  0.0000  0.0000  0.0000
    1HEX    H41   12   1.472   1.384   1.581  0.0000  0.0000  0.0000
    1HEX    H42   13   1.472   1.386   1.418  0.0000  0.0000  0.0000
    1HEX     C5   14   1.307   1.483   1.501  0.0000  0.0000  0.0000
    1HEX    H51   15   1.289   1.539   1.420  0.0000  0.0000  0.0000
    1HEX    H52   16   1.289   1.537   1.583  0.0000  0.0000  0.0000
    1HEX     C6   17   1.214   1.361   1.500  0.0000  0.0000  0.0000
    1HEX    H61   18   1.119   1.392   1.501  0.0000  0.0000  0.0000
    1HEX    H62   19   1.231   1.307   1.418  0.0000  0.0000  0.0000
    1HEX    H63   20   1.232   1.305   1.581  0.0000  0.0000  0.0000
    2HEX     C1   21   1.786   1.639   4.501  0.0000  0.0000  0.0000
    2HEX    H11   22   1.881   1.608   4.500  0.0000  0.0000  0.0000
    2HEX    H12   23   1.768   1.696   4.421  0.0000  0.0000  0.0000
    2HEX    H13   24   1.770   1.692   4.584  0.0000  0.0000  0.0000
    2HEX     C2   25   1.693   1.518   4.499  0.0000  0.0000  0.0000
    2HEX    H21   26   1.711   1.461   4.579  0.0000  0.0000  0.0000
    2HEX    H22   27   1.710   1.465   4.416  0.0000  0.0000  0.0000
    2HEX     C3   28   1.547   1.561   4.501  0.0000  0.0000  0.0000
    2HEX    H31   29   1.528   1.617   4.420  0.0000  0.0000  0.0000
    2HEX    H32   30   1.530   1.615   4.584  0.0000  0.0000  0.0000
    2HEX     C4   31   1.454   1.440   4.500  0.0000  0.0000  0.0000
    2HEX    H41   32   1.472   1.384   4.581  0.0000  0.0000  0.0000
    2HEX    H42   33   1.472   1.386   4.418  0.0000  0.0000  0.0000
    2HEX     C5   34   1.307   1.483   4.501  0.0000  0.0000  0.0000
    2HEX    H51   35   1.289   1.539   4.420  0.0000  0.0000  0.0000
    2HEX    H52   36   1.289   1.537   4.583  0.0000  0.0000  0.0000
.
.
.
.
.
192HEX     C1 3821  22.786  16.639  10.501  0.0000  0.0000  0.0000
  192HEX    H11 3822  22.881  16.608  10.500  0.0000  0.0000  0.0000
  192HEX    H12 3823  22.768  16.696  10.421  0.0000  0.0000  0.0000
  192HEX    H13 3824  22.770  16.692  10.584  0.0000  0.0000  0.0000
  192HEX     C2 3825  22.693  16.518  10.499  0.0000  0.0000  0.0000
  192HEX    H21 3826  22.711  16.461  10.579  0.0000  0.0000  0.0000
  192HEX    H22 3827  22.710  16.465  10.416  0.0000  0.0000  0.0000
  192HEX     C3 3828  22.547  16.561  10.501  0.0000  0.0000  0.0000
  192HEX    H31 3829  22.528  16.617  10.420  0.0000  0.0000  0.0000
  192HEX    H32 3830  22.530  16.615  10.584  0.0000  0.0000  0.0000
  192HEX     C4 3831  22.454  16.440  10.500  0.0000  0.0000  0.0000
  192HEX    H41 3832  22.472  16.384  10.581  0.0000  0.0000  0.0000
  192HEX    H42 3833  22.472  16.386  10.418  0.0000  0.0000  0.0000
  192HEX     C5 3834  22.307  16.483  10.501  0.0000  0.0000  0.0000
  192HEX    H51 3835  22.289  16.539  10.420  0.0000  0.0000  0.0000
  192HEX    H52 3836  22.289  16.537  10.583  0.0000  0.0000  0.0000
  192HEX     C6 3837  22.214  16.361  10.500  0.0000  0.0000  0.0000
  192HEX    H61 3838  22.119  16.392  10.501  0.0000  0.0000  0.0000
  192HEX    H62 3839  22.231  16.307  10.418  0.0000  0.0000  0.0000
  192HEX    H63 3840  22.232  16.305  10.581  0.0000  0.0000  0.0000
 * 24.00000  18.00000  12.00000*



*******************Hexane.gro
20
>     1HEX     C1    1   1.786   1.639   1.501
>     1HEX    H11    2   1.881   1.608   1.500
>     1HEX    H12    3   1.768   1.696   1.421
>     1HEX    H13    4   1.770   1.692   1.584
>     1HEX     C2    5   1.693   1.518   1.499
>     1HEX    H21    6   1.711   1.461   1.579
>     1HEX    H22    7   1.710   1.465   1.416
>     1HEX     C3    8   1.547   1.561   1.501
>     1HEX    H31    9   1.528   1.617   1.420
>     1HEX    H32   10   1.530   1.615   1.584
>     1HEX     C4   11   1.454   1.440   1.500
>     1HEX    H41   12   1.472   1.384   1.581
>     1HEX    H42   13   1.472   1.386   1.418
>     1HEX     C5   14   1.307   1.483   1.501
>     1HEX    H51   15   1.289   1.539   1.420
>     1HEX    H52   16   1.289   1.537   1.583
>     1HEX     C6   17   1.214   1.361   1.500
>     1HEX    H61   18   1.119   1.392   1.501
>     1HEX    H62   19   1.231   1.307   1.418
>     1HEX    H63   20   1.232   1.305   1.581
>    3.00000   3.00000   3.00000   0.00000   0.00000   0.00000   0.00000
> 0.00000   0.00000
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