[gmx-users] multiple molecule interaction

[Mark Abraham]

On 21/07/2011 9:27 PM, smriti Sebastian wrote:
> hi all,
> I am new to GROMACS.I would like to know how we will simulate putting 
> more than two or more molecules of same proteins inside the box and do 
> simulation?Is there any possibility to replace 100 atoms or so of 
> solvent with proteins?

The same way you do it for a single protein. Get a starting 
configuration that suits you, use pdb2gmx on it, and solvate it with 
genbox. There are other approaches you can use if you have pre-existing 
molecule.itp files.

Mark