Dear all
I intend to calculate free energy by using LAMMPS. I have a system including a protein that place into a CNT and entire of system has gone into water. I want to stretch protein out of CNT (in z-direction) slowly with constant velocity by using SMD and calculate work done on protein. then use jarzynski equation to calculate free energy. here CNT has been fixed.
for done work calculation on protein, what should I do? do I dump Fz (force in z-direction) and dz (=Vzdt) for each atom of protein on per step? and sum Fzdz overall atoms of protein?
may you please introduce me literature for the same problem?
Thanks in advance.
Yasti