[gmx-users] Problem of lipid-protein simulation

[Mark Abraham]

Chris Neale wrote:
>  >> But now I want to use the equilibrated bilayer and the peptide
>  >> (simulated in water) together.
>  >> I have inserted the peptide in the bilayer and made a pdb.
>  >> In my pdb file the serial of the coordinates are protein, DPPC, Sol
>  >>
>  >> then I am using the .top file like the following..
>  >> ------------------------------------------------------------------
>  >> #include "ffG43a1.itp"
>  >> #include "ffgmx.itp"

Unless you have reason to know exactly what you're doing, if you're 
including two different force fields to model the same system you should 
be expecting to produce random numbers.

>  >> #include "lipid.itp"
>  >> #include "dppc.itp"
>  >> #include "ions.itp"

Your duplicate atom warnings will probably be occurring because one of 
these files is including one of the ffxxx.itp files, and creating 
duplicates.

Mark