AMBER Archive (2009)

Subject: Re: [AMBER] Partial interactions

Date: Wed Apr 22 2009 - 21:55:52 CDT

Hi Ignacio,

I am not sure if you mean the actual code implementation here or the
resulting model. As for the later, Amber applies the mixed Hamiltonian
V(L) at every single MD step and propagates the system with forces
resulting from it. In the end, there are no 'two' MD simulations, just one
at the given value of Lambda. Also, V(L) is not just linear mixing as you
write under 1) because the softcore potentials are highly non-linear in

As far as the code implementation goes, two independent processes compute
the forces & energies according to V0 and V1, from which the actual
forces, energies and DVDL at the given lambda value are computed in
thermo_int.f. This is complicated a bit if softcore potentials are used,
because then some bonded interactions are removed from the Amber energy
array, not scaled and not contributing to DVDL, plus there is some extra
code in short_ene.f and ew_directe3/4.h to handle the new potential form.

But the important thing is, the processes communicate the mixed forces and
energies and their coordinates progress in sync. So in the end both
processes propagate copies of the same simulation (producing some
superfluous output, but making for an easy implementation).

Kind Regards,


On Wed, April 22, 2009 3:02 pm, Ignacio J. General wrote:
> Thanks for your reply Thomas. I think I'll turn to Tinker since I will
> probably need to do several changes in the code in the near future.
> Before doing that, I still want to do some TI using Amber. But there are a
> few details in the workings of Amber on TI, that I am not sure I correctly
> understand. So, can you please tell me if the following procedure is the
> one
> used by Amber:
> (L means lambda, DL means delta lambda)
> 1) V_L = (1-L)V0 + L V1. This is the new Hamiltonian.
> 2) Run an MD of system V0, with forces scaled by L.
> 3) Run an MD of system V1, with forces scaled by (1-L).
> The simulations above are independent of each other.
> 4) At a given step in the runs, calculate E_V0 - E_V1 m, divide by DL.
> This
> is the dv/dl that appears in the *.out file.
> Questions:
> 1) L (and 1-L) are applied to every force (on atoms in corresponding
> masks),
> or just to Coulomb and LJ forces?
> 2) The evolution of each system, V0 and V1, in their own simulation, are
> guided only by (1-L)V0 or LV1, respectively, right? In other words, the
> Hamiltonian for each simulation is not the whole Hamiltonian V_L, right?

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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