11 votes

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 ...
jheindel's user avatar
  • 3,534
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 ...
Godzilla's user avatar
  • 1,918
8 votes

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{...
wcw's user avatar
  • 1,893
6 votes

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: $$s_{R,6}=1.129\text{, }s_8=0.109$$
Tyberius's user avatar
  • 15.5k
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 ...
Hemanth Haridas's user avatar
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 ...
Shern Ren Tee's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible