[gmx-users] adding parameters for surfactant in topology file

[Erik Lindahl]

Hi,

On Oct 5, 2005, at 7:16 AM, Rahul Karyappa wrote:

> Dear all,
>     I want to run MD on my system containing a 48 repeat unit  
> polymer chain surrounded by 112 molecules of surfactant and several  
> water molecules. I have topology files for the polymer chain and  
> for a single surfactant molecule. Now adding all the topology  
> parameters for all the 112 surfactant molecules is very tedious and  
> time-consuming job. How can I make it simple? Do I need to create  
> an .itp file for the surfactant molecule? PLease guide me for this.

Just create the itp file for one surfactant (x2top might help, but  
there will likely be some manual work too), and then edit the  
molecules section in the topology to say 112 such molecules.

Cheers,

Erik