[gmx-users] cis-trans isomerization

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Fri Jan 30 02:14:00 CET 2004


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?

Any suggestions are welcome.


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