[gmx-users] Free energy pertubation

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Mon Aug 19 22:43:05 CEST 2002

Citando David <spoel at xray.bmc.uu.se>:

> On Mon, 2002-08-19 at 22:04, Pedro Alexandre Lapido Loureiro wrote:
> > Hello, 
> > 
> > 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 Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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