[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)31:217227
E-mail me (or Graham) if you want the source code (it works for Gromacs 2
> 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
>should I add some "-?" option?
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxu at mail.shcnc.ac.cn
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