[gmx-users] Question about water insertion

[Kevin Boyd]

Hi,

You can play around with the -radius and -scale parameters if you're
getting clashes you don't like.

However, it seems like you really should be using gmx solvate. You could
accomplish your goal with

"gmx solvate -cs tip4p.gro -box 10.1103 10.34753 3.9599998  -maxsol 13853"

Kevin

On Fri, Aug 3, 2018 at 7:27 AM, G R <golnaz.chem at gmail.com> wrote:

> I have one water molecule in my gro file as below:
>     TIP4P
>         4
>         1SOL     OW    1   0.054   0.005   0.022
>         1SOL    HW1    2   0.009   0.072   0.073
>         1SOL    HW2    3   0.142   0.041   0.008
>         1SOL     MW    4   0.060   0.018   0.026
>        0.00   0.000   0.000
>     Then use the command bellow to generate 13853 water molecules in the
> box.
>     "insert-molecules -ci water.gro  -box 10.1103 10.34753 3.9599998 -nmol
>     13853 -o insert.gro"
>     But, the water did not settle during energy minimization. When I
> reduced the
>     numebr of water to 5000, it works, but it does not have the correct
>     density. I need 13853 number of molecules. It seems that gmx insert
>     generates water without considering the correct distance between them.
>     Do you have any idea to solve this problem?
>
>     Thank you in advance!
>     Golnaz
> --
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