[gmx-users] Regarding Free energy perturbation

[bipin singh]

When we convert some atoms to a dummy atom (DUM) in a B state topology,
then does the Gromacs free energy code automatically take care of this
transformation in bonded terms (bond, angle, dihedral etc.) because we can
not define B state parameters corresponding to bonded terms of dummy atoms
in a topology.

Another doubt is what would be the option need to be set in mdp file for "
*couple-lambda1*" when we do free energy perturbation through B state
topology:

For example:

At lambda=0,

I have to use:
couple-lambda0=vdw-q (all interactions are on at lambda=0 )

At lambda=1.0,
I am not sure what should be the correct option:

couple-lambda1=none;
I think "none" option will not work here since I am selectively turning off
vdw and charges for few atoms by changing it to dummy atom in B state
topology.


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*--------------------Thanks and Regards,Bipin Singh*