[gmx-users] Building box arround given membrane with gmx solvate. As small as possible.

Vytautas Rakeviius vytautas1987 at yahoo.com
Thu Apr 6 09:48:46 CEST 2017

I want to build box around my membrane with gmx solvate or sth. Ofc. I do not want water in side gap between membrane and box.
I do like this:
gmx editconf -f gap_processed.gro -o gap_newbox.gro -c -bt cubicI expect -d 0 so everything packed in box as tightly as possible, but still after "gmx solvate" I see some water between box and membrane side.Maybe this is normal? Maybe I should do small run to let water flow away? Or maybe my command is wrong and I should make tight box in other way?

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