[gmx-users] Free energy pertubation
A.Villa at chem.rug.nl
Tue Aug 20 09:42:37 CEST 2002
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
> 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,
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
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