[gmx-users] building stacks with a desired system density

[Moeed]

Dear gmx users,

I tried to generate a stack of molecules using

*genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro*


I ran the MD simulation successfully but now I want to change the number of
molecules so that I get the desired system  density. To do so I played a bit
with -dist and -box options but I find it not easy to reach desired
density. I need to have nearly 7 molecules per nm^3.


Regarding genbox program in the literature I see that  it is recommended for
solvation of a solute in water. (The reason I want to try this is because it
seems I can directly enter the number of molecules with -nmol option)



1-I am sorry for asking ridiculous questions but does it make sense if I use
genbox and I ask the program solvate a single hexane molecule with hexane
molecules?

genbox –cp Hexane.gro –cs HExane.gro –p Hexane.top –o solvated.pdb


(although this command line is not working I want to know if there is any
way to modify the command to get it working or my idea is totally wrong!)


2- Initialiy one single hexane molecule is in a box of 3*3*3 nm^3
(Hexane.gro). What is the best approach for doing such calculations. Can I
take any arbitrary box size and then based on the box size put a specific
No. of particles in it so that I get density?


Thank you,




Hexane.gro:


**
Glycine aRginine prOline Methionine Alanine Cystine Serine
   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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