[gmx-users] topology for exited electronic state (dgfd dgdfg)

Groenhof, Gerrit ggroenh at gwdg.de
Tue Jan 2 17:23:48 CET 2018

It is well documented how to construct topologies for ground states of molecules and ions. My task is to simulate the behaviour of dye (anion) after laser exitation in supramolecular complex. Is it possible with standard gromacs force fields?

Yes this is possible. You just need to fit the parameters of torsions, angles, bonds charges etc. onto an accurate potential energy surface. The latter is however, difficult to infer from experiments, and still very challenging for computation due to the multi configurational nature of the wave function in the excited state. Also, the charge distribution can be very sensitive to conformation. Nevertheless, MM force fields have been parameterized for instance for the GFP chromophore (http://pubs.acs.org/doi/10.1021/ct200150r) .

Depending on your research question, however, it may be more convenient to use a direct QM/MM approach to simulate the effect of excitation (http://pubs.rsc.org/en/content/articlelanding/2012/cp/c2cp23628a).

Good luck,


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