[gmx-users] Separate lambdas for repulsive and dispersive free energies?

Michael Shirts mrshirts at gmail.com
Mon Mar 28 05:39:43 CEST 2016

Correct, currently a WCA decomposition has not been implemented.

I'm not sure if I understand this comment, though:

>  For this reason, I only plan to calculate E_vdw_dispersive and E_elec for my system.

E_vdw_repulsive is a gigantic contribution to the solvation free
energy of the protein. Why would you not calculate it?  Without it,
you're calculating something else entirely.

On Sun, Mar 27, 2016 at 8:44 PM, Nuo Wang <wolich22 at gmail.com> wrote:
> Hi all,
> I am trying to calculate the hydration/solvation free energy for proteins
> using free energy perturbation:
> E_hydration = E_vdw + E_elec
> E_vdw (WCA decomposition) = E_vdw_repulsive + E_vdw_dispersive
> However, unlike small molecules, if I turn off both elec and vdw for a
> normal-sized protein, a huge cavity will be created and it will take
> unfeasible amount of time to equilibrate the system. For this reason, I
> only plan to calculate E_vdw_dispersive and E_elec for my system.
> I have read the mailing list posts of implementing the repulsive WCA
> potential in Gromacs, but I have not found any discussion that try to
> implement the WCA-decomposed potential, i.e. repulsive + dispersive, and
> further scaling them separately in free energy calculations.
> According the the manual, it seems that it is impossible to implement the
> decomposition with the Gromacs function form g(x) + f(x). On top of this,
> vdw is scaled together by one lambda. I wonder if I am right on this and if
> there is an alternative way that I am not aware of?
> FYI, the WCA decomposed scaling protocol has been implemented in CHARMM:
> http://pubs.acs.org/doi/abs/10.1021/jp048502c
> Thanks,
> Nuo
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