[gmx-users] Coulomb energies for a charge seperated species

Ali Hassanali ahassana at chemistry.ohio-state.edu
Thu May 14 20:43:33 CEST 2009

Dear Gromacs Users,

I am simulating a system that consists of a tryptophan linked to a thymine 
dimer (two thymine bases stacked together) and am interested in how the 
configurational properties of neutral tryptophan linked to neutral thymine 
compares with tryptophan cation linked to thymine anion.

Using ab initio calculations, I constructed a simple model where I adjust 
the charges on the Trp and on the Thymine dimer so that the overall charge 
of the system is still zero but where the Trp charge is +1 and the thymine 
charge is -1.

I am trying to validate as best as I possibly can, this rather crude model 
so that I can trust the results I am getting and am hoping someone can 
comment or help with this. I have calculated the total Coulomb interaction 
(Coulomb SR+LR) between the Tryptophan cation and Thymine anion over the 
course of a long simulation. Several things that I observe:

* There appear to be 2 distinct states: a charge seperated (by solvent) 
and a charge-charge state where the the cation and anion stack together. 
I would imagine that if you could tether Na+ and Cl- in water with some 
linker, one would see something similar.

* The total coulomb potential energy between the cation and anion 
fluctuates between -50 to -150 KJ/mol. So there is roughly about a 1eV 
coulomb energy difference between the two states. If I take the 
free energy of this coulomb potential energy, the 2 states differ by 
roughly 0.6 kcal/mol (very small). (Please see attached figure). Do these 
fluctuations (range) and energetics seem reasonable?

* As you can see in the attached figure, the Coulomb energy has the 1/r 
trend where r is the distance between the Trp+ and Thymine dimer anion.

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