[gmx-users] FEP

[P]

Yes I'm using soft core potentials:
...
delta_lambda = 0.0
sc-alpha = 1.5
sc-sigma = 0.3
...



Hi,

are you using soft core portentials?
Despite the theoretical drawbacks (see the previous discussion), the
creation/annihilation of atoms was impossible (in my experience) without those
potentials.

Regards.

Pedro.


> Hi all.
> I'm trying FEP In gromacs3.3.  My system (3nm; 3nm; 3nm) consists
> of one Na, Cl, DUM ion and solvent molecules.
> During my free energy calculations I want to perturb:
> 1) Cl-     into a DUM atom
> 2) DUM    into Cl-
>
>
> I'm using ffgmx.  I've added new  atom DUM into ffgmx.atp:
> ...
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