JD Tamucci

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Questions related from JD Tamucci

GROMACS: When and why would one use a PME Interpolation Order larger than 4 or 5?

I’ve come across a handful of tutorials on free energy perturbation (FEP) that use a pme interpolation order of 6, like the one from mdtutorials. It sets the interpolation order value in the...

13 February 2023 2,287 1 View

Error estimate given from "gmx msd"? Is it std deviation or std error? If std error, what's the confidence interval [RESOLVED] ?

I used the gmx msd function to calculate the mean square displacement and estimate the diffusion constant of atoms in my simulations. The *.xvg file reports the diffusion constant and also gives a...

11 February 2019 6,373 3 View