10
votes
Accepted
How exactly does one compute the vibrational density of states from the output of a molecular dynamics simulation?
Ok, I figured out the answer, so I will go ahead and answer my own question.
First, I will provide an overview in bullet points:
[Optional] Generate the velocities at evenly spaced frames from the ...
- 3,464
9
votes
What is autocorrelation time?
The autocorrelation time comes from the statistical analysis of ergodic systems, where one is interested in obtaining statistical averages of an observable $A$ by drawing samples from a distribution ...
- 1,918
8
votes
Accepted
Derivation on correlation function and response functions in polymer physics
It looks Doi makes some extra simplifications (beyond expanding the exponential) that are valid when the external field is weak.
Let's start with what you wrote and make one simplification,
$$
\begin{...
- 1,873
5
votes
Accepted
VdW-D3 correction with HSE06 functional in VASP
There is a DFT-D3 implementation from the Grimme group on Github that has a parameter file containing these values for HSE06. From here, it seems that for HSE06:
$$s_{R,6}=1.129\text{, }s_8=0.109$$
- 15k
4
votes
Effect of trajectory length and resolution on the Residence Time
The autocorrelation function (HBond or any other property) gives you the time that takes the system to forget that state. If the length of your analysis window in trajectory is less than the ...
- 2,612
1
vote
Programming auto-correlation function calculation
I cannot comment on the Fortran code, but in general, calculating the integrated autocorrelation correctly is a subtle exercise. There is increasing uncertainty in estimating correlation at increasing ...
- 2,498
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