Dipole:
describe at
the atomic detail, the interactions governing the behavior of molecules. Despite the interests
and useful information that we can obtain from a normal MD, sometimes it is necessary to
make some changes to observe some specific behaviors. In this job we modified a
standard MD and propose two method to
fix the orientation of a molecule’s dipole, allowing us observe how the dipole orientation of
some residue
affects the system. The first method is based on an harmonic restraint over the dipole and the
second method is based
on an applied electric field over the molecule. It is also important to say that we propose a
new collective variable, the dipole.
Notice that in a non
modified system the orientation and position of a dipole may change by a electric field or by
an interaction with a
charged molecule, residue, atom or system, so orientate the dipole in a chosen direction give
us the chance to
simulate one of the latest described phenomenon. This method has been tested in solvated
and non-solvated system, orientating
the dipole of a water molecule, arginine, methanol and ethanol. Also, like a test, was running
a Local Elevation (LE) metadynamics to plot the free energy
perturbation (FEP) of the system.
The implementation of this methods have been developed in Colvars (github.com/colvars) module of NAMD and LAMMPS.