[gmx-users] free energy for converting DUM into Ar

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Mon Sep 29 19:13:01 CEST 2003

If a free energy calculation requires annihilation or creation of atoms
one could use soft-core potentials(See Molecular Modeling Andrew Leach 2
ed. p 579)) to prevent singularities in the potential. 

The softcore  Lennard Jones Potential for states A and B in gromacs is
as follows:

Vsc =  

at lambda equal to 1 or 0 the potential is just the Lennard Jones
potential of either state A or state B. All of  the states in between A
and B are soft core states which don't have a singularity at r = 0.

In order to implement this in Gromacs using the 
free_energy      = yes
option, one must first decide if they are going to do Multi
Configuration thermodynamic integration(MCTI) or Single Configuration
thermodynamic integration(SCTI).See( J. Chem Phys 95(2), 15 July 1991).

In MCTI one would set delta_lambda = 0 and rerun the calculation at
fixed intervals of dLambda.

In SCTI one would usually set delta_lambda to 1/(Total Simulation Time)
and then hope their total time is long enough to achieve convergence.

There are advantages and disadvantages to both.  

The sc_alpha value should be chosen such that "the position of the
minimum in the soft-core potential coincides with that of the unscaled
energy curve"(Leach)

One thing that I don't believe is implemented yet in Gromacs is
dynamically scaled Lambda values. This should be fairly straight forward
to implement. (i.e. Lambda = (t/(Total simulation time))^n).

Hope This Helps


On Sun, 2003-09-28 at 22:33, Anton Feenstra wrote:
> Ilya Chorny wrote:
> > I figured it out.
> Perhaps, for the sake of those searching the archives for answers,
> you could post a short summary of what you did?
Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
Postdoctoral Researcher   University of California-San Francisco
phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
fax: (415)502-1411        San Francisco, Ca, 94107
            email: ichorny at maxwell.ucsf.edu

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