[gmx-users] Free energy pertubation

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Mon Aug 19 23:22:41 CEST 2002

> > > 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
 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 Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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