Dear All
I want do calculate the binding energy of a biomolecule in vacuum adsorpted at a LJ9/3 wall for different wall seperations. First of all I have calculated the total energy of the molecule alone to later substract it from the total energy of the system: molecule + wall. For this I have used the lammps command minimize. Unfortunately after the minimization has stopped, there is nothing written in my dump file.
So has my energy not converged?
What I have done wrong?
A second question is whether using the minimize command is the right way to compute the binding energy? Besides one can only regard one fixed orientation of the molecule with respect to the wall as rotations are not acccount for in the minimization process.
I also tried to set up a simulation to get the free energy by accounting in addition for the orientation of the molecule. But using NVT the total energy of the system always completely drifted away. When I do the same simulation including also 900 water molecules in my system there was no problem with energy drift. So my further question:
Is lammps able to simulate very small systems (23 atoms) with high fluctuations?
Best regards Sabine
data_4.5 (9.48 KB)
in.phe_prod (746 Bytes)
log.lammps (20.9 KB)
Dear All
I want do calculate the binding energy of a biomolecule in
vacuum adsorpted at a LJ9/3 wall for different wall
seperations. First of all I have calculated the total energy of
the molecule alone to later substract it from the total energy
of the system: molecule + wall. For this I have used the
lammps command minimize. Unfortunately after the minimization
has stopped, there is nothing written in my dump file.
So has my energy not converged?
What I have done wrong?
Did you tell LAMMPS to write something to the dump file? Do
you get any error messages in the log files?
I also tried to set up a simulation to get the free energy by
accounting in addition for the orientation of the molecule. But
using NVT the total energy of the system always completely
drifted away. When I do the same simulation including also 900
water molecules in my system there was no problem with energy
drift. So my further question:
Is lammps able to simulate very small systems (23 atoms) with
high fluctuations?
I have simulated single molecule (10 to 30 atoms) systems in
LAMMPS with no problems.
Were you careful about how you set up your very small system?
Did you take into account things like cut-offs relative to box
size or turn off periodic boundary conditions for a tiny,
single molecule system? Did you select an appropriate timestep
size for both systems?
Joanne Budzien