Hello,
I am going to simulate a single layer of graphene in NPT ensemble, and I have defined <h^2> in order to provide a quantitative description of the roughness of its surface. However, I have no idea about what the value of the damp parameters should be in “fix npt” related to thermostat and barostat. I am getting different mean value of the <h^2> and fluctuation patterns of it when I am changing the damp parameters such as 10, 100, 1000 while I really got confused which one is the proper one.
Does anyone know how can I estimate the proper value of these parameters in my case? what about the timestep, does it plays a role in determining damp values?
In advance, I appreciate any help
Regards,
H. Gh. Kalashami
From fix npt doc page, “For all barostat keywords, the Pdamp parameter operates like the Tdamp parameter, determining the time scale on which pressure is relaxed. For example, a value of 10.0 means to relax the pressure in a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see the unitscommand).
IMPORTANT NOTE: A Nose-Hoover barostat will not work well for arbitrary values of Pdamp. If Pdamp is too small, the pressure and volume can fluctuate wildly; if it is too large, the pressure will take a very long time to equilibrate. A good choice for many models is a Pdampof around 1000 timesteps. Note that this is NOT the same as 1000 time units for most units settings.”.
Please double check whether your 10, 100, and 1000 are “timesteps” or “time units”.
Ray
Hello,
I am going to simulate a single layer of graphene in NPT ensemble, and I
there is no such thing as an NPT ensemble for such a system.
have defined <h^2> in order to provide a quantitative description of the
what is <h^2> in this context?
roughness of its surface. However, I have no idea about what the value of
the damp parameters should be in "fix npt" related to thermostat and
barostat. I am getting different mean value of the <h^2> and fluctuation
patterns of it when I am changing the damp parameters such as 10, 100, 1000
while I really got confused which one is the proper one.
since this appears to be such an important issue for your study,
perhaps you should spend some time trying to understand how a
nose-hoover thermostat and barostat work. it is very difficult to give
specific advice on very vague information, you don't even mention what
units you are using for those numbers, let alone describe the process.
there is a good chance that what you are seeing is less an impact of
the choice of damping parameter directly, but a consequence of
unsuitable system setup and/or equilibration.
Does anyone know how can I estimate the proper value of these parameters in
my case? what about the timestep, does it plays a role in determining damp
values?
yes and no. the time step primarily determines whether you have a
reasonably accurate time integration. but it also somewhat determines
the order of magnitude of a reasonably choice of the damping
parameters. they need to be chosen so that you can a reasonable but
not too tight coupling of the nose-hoover chains to the system. if it
doesn't couple, there is no transfer of energy, if it couples too
tightly, the thermostat modifies your dynamics. of course for rigid
systems this can be tricky. for details, please see the corresponding
literature.
axel.