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.
Ali
<<attachment: benchtrpcat.jpg>>
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