[gmx-users] Insertion of polymer into bilayer

[Mark Abraham]

varsha gautham wrote:
> Dear all,
> 
> Thanks for all your valuble suggestion in helping me to build
> polymer.I sucessfully built the polymer and its working fine without
> any issue.
> Now my next step is to insert the polymer in aqueous phase of a lipid
> bilayer.How can i do that with gromacs?,since am a new user to
> gromacs,please give me detailed procedure on this.THanks a lot in
> advance.

Solvating a structure is a basic procedure in GROMACS - you should look 
at some tutorial material and see how genbox can be used.

I would approach your problem by taking a pre-equilibrated bilayer and 
stripping away the waters. Then judicious use of editconf on that 
coordinate file and your polymer coordinate file will have sets of 
coordinates in both that correspond to the polymer being in the gap left 
by the water. Then you can either paste in your polymer with a text 
editor (updating the atom count in the .gro file appropriately, see 
http://www.gromacs.org/documentation/reference/online/gro.html), or try 
"solvating" the polymer with the membrane file with genbox. Then finally 
solvate the lipid+polymer with genbox in the normal fashion.

This will not be easy for a beginner. You should consult 
http://wiki.gromacs.org/index.php/Membrane_Simulations, and read the man 
pages for genbox and editconf thoroughly. Good luck!

Mark