Dear Experts
I have a non-periodic box of a protein which I hope to minimize and get the minimized energy. I realized that the total coulombic energy thus the total energy is different with different cut-off values for coul/cut term, is there a way to minimize the system without the coulombic cut-off considering the all possible pair interactions.
best
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA
It's up to you to define the energy model you are trying
to minimize. If you want to use a potential function w/out
Coulombic terms (e.g. just LJ), you can. Whether that
makes any sense for a protein with charge is also up to you.
Steve
Dear Experts
I have a non-periodic box of a protein which I hope to minimize and get the
minimized energy. I realized that the total coulombic energy thus the total
energy is different with different cut-off values for coul/cut term, is
there a way to minimize the system without the coulombic cut-off considering
the all possible pair interactions.
LAMMPS doesn't have a way to bypass the neighborlist.
you'd have to increase the coulomb cutoff until the energy
is converged (or you run out of memory) through covering
all interaction pairs.
i don't think it makes a lot of sense though.
with proteins you have a very rugged potential
energy hypersurface and it is practically
impossible to determine a "good" minimum at all.
also, in practice, the *free* energy, which considers
the probability of reaching a certain state, matters
*much* more than an absolute potential energy.
furthermore, if your protein is solvated, then you also
have the problem that each individual solvent molecule
added or removed would change the total energy as well.
it is a lose-lose scenario.
axel.