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.