7 votes
Accepted

What's a quick way to get a molecular bond length using a Newtonian model?

The quality of force fields depends a lot on the parameters. For example, if I use Avogadro and draw out O=O and optimize using the default (MMFF94) I get an O-O distance of 1.282 Å. If I optimize ...
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3 votes

Determining bond angle from infrared spectra?

This is done the same way that bond length is determined from infrared spectra. We fit the spectra to a potential energy surface (PES), such that when the PES is fed through the Schroedinger equation, ...
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3 votes

How to calculate diffusion coefficient from MSD graph using GROMACS?

If you can obtain the raw data used in that plot, as a purely statistical and numerical exercise you can determine the interval which will give you minimum uncertainty in the estimate of the gradient. ...
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3 votes
Accepted

How to calculate diffusion coefficient from MSD graph using GROMACS?

MSD accuracy decreases as a function of the lag-time $t$, because for large $t$ there are fewer pairs of time slices of interval $t$ to average over. Think of the limit in calculating MSD for the ...
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  • 568
1 vote
Accepted

I have a force in eV/Angstroms. How do I convert it so that the speed I calculate is in Angstroms/second?

Applying a force $F$ acting on a mass $m$, the acceleration according to classical mechanics is: $$\tag{1} a = \frac{F}{m}. $$ Given the speed $v(0)$ at time $t=0$ and the acceleration, we can obtain ...
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1 vote

Computing phonon dispersion from molecular dynamics simulations?

I think one could try to utilize a functionality of hiPhive or TDEP to fit the data from MD-simulations. hiPhive is probably an easier way since it is installed pretty easy using pip. In case of ...
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