Dear administrator:
I've been trying to use lammps to reproduce the Martini simulation.
But with the inputs I wrote, my particles simply vibrate to their origin position, never did they move from there lattice sites.
Here I put both the input script and input data file.
I will be appreciated if you can give me some reference.
Di
input.hydrogel (1.37 KB)
input.data (1.85 MB)
Dear administrator:
I've been trying to use lammps to reproduce the Martini simulation.
But with the inputs I wrote, my particles simply vibrate to their origin position, never did they move from there lattice sites.Here I put both the input script and input data file.
sorry, but it is unlikely that somebody will look into this.
I will be appreciated if you can give me some reference.
i would recommend to start with some very simple test
systems. what you describe sounds a lot like you
used wrong conversion factors for parameters.
are you sure that you have all units correct?
axel.
I think Axel might be right. Perhaps you have a unit conversion
problem. The energies and temperatures of your system are not
compatible somehow. I tried running your simulation, both at the
original temperature (310) and at high temperature (2000). The
polymers are able to move dramatically at high temperature (2000). So
there is no problem with the commands you used to evolve your system.
(Details: For the high-temperature test, to keep the system from
boiling, I used NVT, not NPT. I did run the system at low temperature
first to equilibrate the volume to something reasonable beforehand.)
Good luck.
Hydrogels are cool.
Andrew
You're energy values are too large.
I just remembered that Gromacs users typically specify their energies
in kJ/mole, and almost everybody else in the classical-MD world uses
kCal/mole. The group that created Martini use gromacs, and I think
that all of their epsilon enegy parameters are in kJ/mole. (Edit:
they are. I just checked.)
Your LAMMPS simulation assumes you are using kCal/mole (because you
are using: "units real"), so divide all of your energy parameters
(both epsilon, and the various K values) by 4.184 and see if that
helps.
Cheers!
Andrew
also gromacs uses nanometers instead of angstroms. Axel.