[gmx-users] cis-trans isomerization

[Anton Feenstra]

Martina Bertsch, PhD wrote:

> Greetings.
> 
> Activation of bovine rhodopsin in the POPC bilayer has been simulated by 
> allowing the cis-trans isomerization in the ligand retinal [Saam et al., 
> Biophys. J. (2002) 83: 3097-3112]:
> 
> "...Retinal was isomerized around the C11=C12 double bond by transiently 
> switching the dihedral potential energy function of this bond from the 
> ground state form to the "isomerization" one, which resulted in an 
> 11-trans retinal in ~150 fs. After isomerization, the dihedral potential 
> was switched back to its ground state form, and a 10-ns simulation was 
> carried out... The dihedral potentials in the chromophore chain are 
> cosine functions having minima at 0° and 180°. Due to the strong 
> electronic delocalization effect in retinal, particularly in the 
> protonated form the barrier against the rotation of individual bonds 
> along the chain differs from the barriers expected for pure single and 
> double bonds... In the ground state, the applied potential function 
> separates these two isomers by a barrier of 35 kcal/mol. To induce the 
> isomerization, we transiently (for 200 fs) switched the C11=C12 dihedral 
> potential to one with a single minimum at 180°. In the 11-cis 
> conformation (0°) the new potential has a maximum that is ~42 kcal/mol 
> higher than the corresponding minimum in the ground state potential. 
> Thus, by switching to the "isomerization" potential we instantly add 
> this amount of energy to the system. The potential shape is described in 
> Hayashi et al. (2002). From the seven cosine Fourier components therein 
> we used only the three largest ones, which are sufficient to reproduce 
> the general features of the potential energy curve, such as the plateau 
> region observed in ab initio molecular orbital calculations. This 
> description maps the transition from an excited-state potential through 
> a conical intersection back to the ground state onto a one-dimensional 
> potential energy, with the dihedral angle as the only variable..."
> 
> How do I program the transient switching of the dihedral potential 
> energy function for a double bond in a receptor-bound ligand in Gromacs?

Choose different parameters for the dihedral in your .top (or .itp) file,
and run. Next, you can switch back to original parameters.

Alternatively, you could use the FEP options, and put your alternate
parameters in the 'B' section of the topology. This is in the manual
(mostly...).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|