Hi,

I am doing a simulation of polymer system at different temperatures.

The simulations

use FENE potential and LJ potential with LJ units. I don't know how to

set the proper

damping parameters in Nose-Hoover algorithm when using fix nvt or

Pdamp parameter

using fix npt. Could anyone give me some hints? Thanks!

Zhimin Xiong

Zhimin,

I use real units therefore whatever the number I enter is in femtoseconds. In lj units, I believe you need to use the reduced time unit:

t* = sqrt(eps/mass/sigsq).t

eps and sig are your lj parameters. sigsq is the sigma square. sqrt is for squareroot.

I looked for the best parameter along with my timestep that kept the pressure constant by trying different numbers.

Hope this helps,

Burcu

Hi. Actually the unit of LJ time is tau_LJ = sqrt(m*sigma^2/epsilon) - do

the dimensional analysis.

As far as the temperature damping time, a typical time is of order 1

tau_LJ. This time should be at least of order 100 timesteps.

For the pressure damping time, there are various ways of selecting it. Do

you want the system to be overdamped or underdamped? You need to think

about what you want it to be in terms of the stress relaxation times of

the system. I tend to set it to of order the fastest stress relaxation

time, which is the time for sound to propagate across the system

diagonally. Also, this time should be large compared to the temperature

damping time. The sound velocity is something like 4 sigma/tau_LJ.

Best,

Rob

Thanks to Rob and Burcu!

Your explanations are very helpful!

Best regards,

Zhimin