[gmx-users] How can i specify a user defined potential between i, i+2 residues

[Mark Abraham]

On 16/05/2012 3:43 PM, mohan maruthi sena wrote:
> Hi all,
>           I use a user defined potential to describe non-bonded 
> interactions, as this excludes i, i+2,i+3. If i want to describe a 
> user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can 
> i give that in mdp file.

Doing that with a user-defined non-bonded potential requires you change 
nrexcl for your force field. Doing that with a user-defined bonded 
potential doesn't, but you'll have to specify all the interactions manually.

Mark