[gmx-users] about water molecules in popc

Jose D Faraldo-Gomez jdfg_gmx at hotmail.com
Thu May 30 11:04:11 CEST 2002

If the problem is waters in the lipid tail region, you could either remove 
them with a script, or have a local copy of genbox's input file vdwradii.dat 
(or something like that) with increased values for the radii of carbons in 
the lipid tails, so that the 2 leaflets effectively overlap and no waters 
can be added there.

If the problem is the interface with the protein, Graham Smith and myself 
developed a methodology to optimise the lipid-protein contacts in membrane 
protein simulations. The reference is

European Biophysical Journal
Eur Biophys J (2002)31:217–227

E-mail me (or Graham) if you want the source code (it works for Gromacs 2 


>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 
>         (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
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

MSN Photos is the easiest way to share and print your photos: 

More information about the gromacs.org_gmx-users mailing list