[gmx-users] Free energy calculation of multiple solutes

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 04:36:01 CET 2014

On 2/19/14, 1:05 PM, Jeff Chen wrote:
> Dear All,
> I am trying to calculate the change in free energy that occurs when
> charging multiple type B molecules in an A-B mixture. For example, I have a
> mixture of 900 molecules of type A and 100 of type B. When coulomb
> interactions are on, B is identical to A (something like TIP4P water), but
> when coulomb interactions are off, each B is simply a Lennard-Jones
> particle (in the topology file, I've labelled B differently and called the
> molecule SOLB, but all interaction information is identical to A). To do
> the free energy calculations, I perform different simulations at each
> lambda point. For example, for a simulation with lambda=0, I have the
> following in my .mdp file:
> free_energy = yes
> init_lambda = 0.0
> delta_lambda = 0
> foreign_lambda= 0.05
> couple-lambda0=vdw-q
> couple-lambda1=vdw
> couple-moltype=SOLB
> and when lamba=1,
> free_energy = yes
> init_lambda = 1.0
> delta_lambda = 0
> foreign_lambda= 0.95
> couple-lambda0=vdw-q
> couple-lambda1=vdw
> couple-moltype=SOLB
> I expected that when lambda=0, B molecules would behave identically to A
> molecules with the coulombic energy fully turned on (couple-lambda0=vdw-q),
> and when lambda=1, B molecules would behave like LJ particles, with no
> coulombic interactions, either with each other, or with A molecules.
> However, when I look at the coulombic energy for B-B interactions (I used
> tpbconv -o to make a new *.tpr for only B molecules, then used mdrun -rerun
> with a trajectory containing only information about B molecules), I find
> that both the short-range and reciprocal coulombic energies are NOT zero as
> I had expected for lambda = 1, and are in fact exactly equal to the
> negative of the respective coulombic energies obtained using the same
> trajectory data when lambda=0.

What are the energies without using tpbconv and mdrun -rerun?  In other words, 
it's necessary to figure out whether this is a problem in the original 
simulation with the free energy code (unlikely, given how simple the system is) 
or a problem using mdrun -rerun in conjunction with the free energy code (far 
more likely).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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