[gmx-users] FEP

P pyt1 at op.pl
Thu Mar 30 14:53:36 CEST 2006

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


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



> 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:
> ...
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060330/2e08b681/attachment.html>

More information about the gromacs.org_gmx-users mailing list