If you can't write a script, then do the minimization and equilibration with
water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or
use constraints in the z dimension (posre.itp force constant 1000 along z and 0
along x and y). This will stop it from going into the membrane.
Hi ChrisThank you for your suggestions!These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out.
I'm trying to use the method you suggested, I
It is unclear why your second method works for you. However, given that it does,
just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3
and then use your own script to remove any spc waters that were put inside the
membrane and modify the nubers in your topology file accordi
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