[gmx-users] Solvation of the bilayer

[Alex]

What are the dimensions of your bilayer and your box, and where do the 
water molecules go?


On 5/28/2018 12:20 AM, Amali Guruge wrote:
> Dear Gromacs users,
>
> I have a bilayer in xy plane. I tried to solvate the bilayer
> (sur_bilayer.pdb) with water molecules using gmx solvate. I used the
> command;
> gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb
>
> However, water molecules are not distributed in the hydrophilic layers in
> the xy plane as I wanted. How can I solve this problem?
>
>
> Thank you.
>
> <name.surname at monash.edu>
>
> <name.surname at monash.edu>