Dear all,

I want to simulate a mesoscopic polymer model of DNA in the standard condition (298K, 0.01 NaCl Molar, 7 phH) based on the parameters given in this article. I follow the steps in the article and map from the SI unit to LJ unit in the following way:

- \sigma=2.5nm\sim7.0 \text{base pair}
- \epsilon\sim298*k_B
- m\sim4777\text{dalton}
- \tau\sim0.1ns

The authors then say if the Stokes-Einstein formula

D=k_BT/\zeta=k_BT/m\gamma=k_BT/3\pi\eta\sigma

is used, then one simulation time unit is \tau_D=\sigma^2/D=35ns=350\tau (diffusion time) in water with viscosity \eta=0.001 \text{Pa.s} at T=298. They then set dt=0.01\tau_D=0.35ns=3.26\tau.

However, the authorsâ€™ explanation is vague when they talk about the friction coefficient \zeta in the Langevin thermostat: They first say damping factor \zeta=m\gamma\sim0.5 with m=1 and then say \zeta=k_Bt/D. If we use the above numbers, then zeta\sim2.36\times10^{-11}kg/s, \gamma=2.97\times10^{13}s^{-1} and damping time \tau_{\gamma}=1/\gamma=3.36*10^{-4}ns\sim0.003\tau and if dt=0.01\tau_D, then it is \tau_{\gamma}\sim10^{-2}dt â€“ \tau_{\gamma} is the **tdamp** in Langevin thermostat.

However, I know that \tau_{\gamma} should be in range from 0.1\tau^{-1} to \tau^{-1} if we want to study a single polymer in a good solvent; moreover, we should use dt\ll\tau_{\gamma} ; for instance, dt=0.005\tau. I also know that we need to remove the overall diffusion caused by the Langevin thermostat if we want to study diffusion of polymers and for instance, test the Rouse dynamics (See Grest and Kremer 1990).

I am now confused; what is the value of tdamp (or \tau_{\gamma})?

Does one measure \tau_{\gamma}\sim0.003\tau in the sampling phase when the contribution due to \tau_{\gamma}=0.5\tau of the Langevin thermostat is removed?

I know the detailed calculation above is probably confusing itself, so it is probably better to ask my question this way:

If I want to be able to compare the diffusion coefficient I measure in an MD simulation with an experimental one; how I have to set the tdamp in the Langevin thermostat?

Thanks an advance for your response.

Kind regards,

Amir