[gmx-users] Free energy pertubation

[Pedro Alexandre Lapido Loureiro]

> > > 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. 
 
 

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil