[gmx-users] about water molecules in popc

Xu Yong yxu at mail.shcnc.ac.cn
Thu May 30 03:08:59 CEST 2002

Dear users,
  I am new user to this package. I wanted to use the POPC coordinate build by Tieleman. an equilibrated popc bilayer with 128 lipid molecules was used. I made a cylindrical  hole  in the center of the bilayer. The protein was inserted into the cavity.when this system was solvated with spc waters  the h2o molecules was also be added to the space of popc but this is unreasonable. It should outside the popc. should I delete these water molecules by hand? or there are any other way to solve this.
     I used the command:   (1)editconf -f protein_popc.gro -o protein_popc_box.gro
        (2)genbox -cp protein_popc_box.gro -cs -o protein_popc_box_wat.gro -p protein.top
should I add some "-?" option?

Xu Yong
        yxu at mail.shcnc.ac.cn

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