Hi all,
I am simulating a system of surfactants in water in NPT ensemble and I would like to use more than one thermostats, one for each group of atoms, as that can takes care of some of the problems associated with global thermostats.
I was wondering how I can use the Nose Hoover chain thermostat for each group? Is there any command like fix temp/rescale or fix temp/berendsen for NH?
Thank you,
Mona
Hi all,
I am simulating a system of surfactants in water in NPT ensemble and I would like to use more than one thermostats, one for each group of solvent and surfactans, as that can takes care of some of the problems associated with global thermostats.
I was wondering how I can use the Nose Hoover chain thermostat for each group? Is there any command like fix temp/rescale or fix temp/berendsen for NH?
Thank you,
Mona
Hi all,
I am simulating a system of surfactants in water in NPT ensemble and I would
like to use more than one thermostats, one for each group of atoms, as that
can takes care of some of the problems associated with global thermostats.
what problems?
I was wondering how I can use the Nose Hoover chain thermostat for each
group? Is there any command like fix temp/rescale or fix temp/berendsen for
NH?
technically, there are several options, but there are
several constraints.
- pressure control has to be global
- there can be only one time integrating fix per atom
the nose-hoover based fixes do include the integrator,
all others don't.
on top of that comes the question of how meaningful
such a heavy multi-tiered thermalization is going to be,
and - of course - your system will not be in a known
statistical mechanical ensemble.
axel.
Hi Axel,
I want to control the temperatures of the solute, and solvent independently,
by using only fix npt, the tempraute of the solute noticeably is lower than the solvent.
I can not use the NH thermostat with fix NPT, or any other integrating fix, right?
Can I use the temp/rescale with npt? like each group are ,
fix 1 all npt temp 300 300 100 aniso 1.00 1.00 1000
fix 11 SOL temp/rescale 100 300 300 0.5 1
fix 12 SUR temp/rescale 100 300 300 0.5 1
Does this make sense?
Regards,
Mona
Hi Axel,
I want to control the temperatures of the solute, and solvent independently,
by using only fix npt, the tempraute of the solute noticeably is lower than
the solvent.
this should not be. that means that either you are not computing
the temperatures correctly, or that your system is not properly
equilibrated. mind you, that it doesn't matter how you get to
equilibrium and you can do all kinds of strange tricks.
if you don't have good equipartititioning of the kinetic energy,
you should first run with fix nve and fix langevin to have better
dissipation of kinetic energy. if you are really careful, you start
with a "short" time constant for fix langevin and then make it
larger in 1 or more stages and then transition to a nose-hoover
chain thermostat.
I can not use the NH thermostat with fix NPT, or any other integrating fix,
right?
Can I use the temp/rescale with npt? like each group are independently
coupled to a heat bath,
fix 1 all npt temp 300 300 100 aniso 1.00 1.00 1000
fix 11 SOL temp/rescale 100 300 300 0.5 1
fix 12 SUR temp/rescale 100 300 300 0.5 1Does this make sense?
no, this doesn't make sense for two reasons.
1) now you have two fixes adjusting kinetic energy
and every time temp/rescale acts, it throws the
nose-hoover thermalization off balance.
2) the settings for temp/rescale seem far too tight
and temp rescale does more damage for equilibration
since it doesn't change the distribution between
hot and cold atoms and basically gives your system
a kick every time is is executed
there have been repeated discussion on this list about
good strategies for equilibration, how to compute
temperature correctly, and what are acceptable
temperature fluctuations. it looks to me, it would be
very helpful for you to search the mailing list archives
and read up on them to make a better informed choice
of how you set up your simulation(s).
cheers,
axel.
I'll just add that you are combining a barostat
with a thermostat in a confusing (and incorrect)
manner, as Axel says.
You could use fix nph for the barostat, and then
thermostat independently with whatever LAMMPS
thermostat you wish.
Steve