[gmx-users] Free energy pertubation

[Alessandra Villa]

On Mon, 19 Aug 2002, Pedro Alexandre  Lapido Loureiro wrote:

> > > > I want to use the FEP method to insert molecules in a DPPC bilayer, by
> > > slowly
> > > > growing them.
> > > > I have followed the instructions on the manual (two sets of parameters
> > for
> > > the
> > > > same atoms in the .itp file and free_energy=yes in the .mdp file).
> > > > I think this will tell GROMACS to grow the molecules while lambda is
> > > increasing
> > > > by delta_lambda.
> > > > Am I right?
> > 
> > 
> > > In principle yes. Have you tried it out yet?
> > 
>  Yes, but it did not work :(
>  Another idea would be to set the atom mass to zero in the parameter A and to
>  use
>  the full mass as the parameter B, but grompp does not accept it.
>  I could do that with LJ parameters but ... how?
>  
>  Thanks for your reply,
>  
>  Pedro. 
>  

Hi, 

did you put free_energy=yes and delta_lambda not equal to zero? 

Are the LJ parameters or the charges of state A  different from the one 
of state B? 
 
If they are the same non-bonded parameter and the same mass you will have
no pertubated atom ( as you can observed in the log file). 
 
As a check you can try to see if your topology works giving a fix
parameter to lambda and delta_lambda=0. 
and looking if the atom are perturbated in the log file 

best regards 

Alessandra