Dear lammps users
In a system formed by a metallic nanotube, a peptide and water I am trying to equilibrate, using the following configuration:
#===============================Minization =====================================================
minimize 1.0e-4 1.0e-8 1000 10000
#============================= Equilibration=====================================================
fix 1 all nvt temp 300.0 300.0 $(5.0*dt)
fix 2 all setforce 0.0 0.0 0.0
dump 1 nanotube custom 5000 dump_Nanobute.lammpstrj id mol type x y z
dump 2 fibril custom 5000 dump_fibril.lammpstrj id mol type x y z
run 500000
However, I obtain static values, the temperature is zero and the energy values do not change at each step of time.
My goal is to equilibrate the system with the only condition of restrained positions, is it possible to use fix rigid / nvt for this case?
Sincerely
Eduardo
Dear lammps users
In a system formed by a metallic nanotube, a peptide and water I am trying to equilibrate, using the following configuration:
#===============================Minization =====================================================
minimize 1.0e-4 1.0e-8 1000 10000
#============================= Equilibration=====================================================
fix 1 all nvt temp 300.0 300.0 $(5.0*dt)
fix 2 all setforce 0.0 0.0 0.0
dump 1 nanotube custom 5000 dump_Nanobute.lammpstrj id mol type x y z
dump 2 fibril custom 5000 dump_fibril.lammpstrj id mol type x y z
run 500000
However, I obtain static values, the temperature is zero and the energy values do not change at each step of time.
that is to be expected, you do not set an initial velocity and with fix setforce to reset all forces to zero.
due to no forces there cannot be any change in velocity (and thus kinetic energy) and due to no initialization there are no velocities at all.
My goal is to equilibrate the system with the only condition of restrained positions, is it possible to use fix rigid / nvt for this case?
neither fix setforce nor fix rigid is the correct tool for this. if I understand you correctly, you want atoms to be able to move around their initial position, but be restrained and not move around. that would be achieved with fix spring self.
mind you that this is not quite the same as a proper equilibration, but it will equilibrate for the system under the restraint. if the system will “want” to be in a very different configuration, then the position restraint will prohibit that and thus prohibit equilibration. but then again, that is more a question of what is a meaningful model and not so much a question of what are the suitable LAMMPS commands.
axel.
Thank you Professor Axel, your explanation was very good.