[gmx-users] Question about water insertion

G R golnaz.chem at gmail.com
Fri Aug 3 13:27:52 CEST 2018


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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