Martínez Molecular Modeling Group

packmol

Packmol - Initial configurations for molecular dynamics simulations

JuliaNotes.jl

A collection of examples and explanations about Julia

CellListMap.jl

Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.

EasyFit.jl

Easy interface for obtaining fits for 2D data

2021_FortranCon

Simulation codes shown at the FortranCon 2021

jlcode_example

Example of the use of jlcode and the JuliaMono font to write Julia code in LaTeX

SPGBox.jl

Spectral Projected Gradient Method for Box-Constrained Minimization

Packmol.jl

The future of Packmol

ComplexMixtures.jl

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

PDBTools.jl

Simple structure and functions to read and write PDB files

FundamentosDMC.jl

Material para el curso Fundamentos de Mecánica Estadística y Simulaciones: Simulación Computacional Avanzada en Química, Bioquímica y Ciencias de Materiales. CELFI/Universidad de Buenos Aires

lovoalign

MolecularMinimumDistances.jl

Computes the set of minimum distances between to sets of particles, which can be grouped (like in molecules).

MolSimToolkit.jl

A set of tools for analyzing molecular dynamics simulations

SolventShellInteractions.jl

Computes the interaction potential between a solute and the solvent molecules having at least one atom within a cutoff distance from the solute.

XEMMSB2021

Files for XEMMSB2021

BlockAverage.jl

Computes the block average and error of the mean of (time-dependent) data.

PackmolInputCreator.jl

Package to help creation of Packmol input files for mixtures.

MDLovoFit.jl

Julia wrapper for the MDLovoFit package

stride

The original implementation of the structure identification (STRIDE) algorithm to identify protein secondary structure elements

CellListMapArticleCodes

Code blocks of the CellListMap paper.

ComplexMixturesExamples

Examples provided for the ComplexMixtures package.

2023_AFP-LM_BpdA

2024_Ramos_Martinez_BGHI

Data for Ramos, Martínez, 2024

atd_scripts

Anistropic Thermal Diffusion scripts - http://leandro.iqm.unicamp.br/atd-scripts

AtomDistances.jl

Simple script to illustrate how to compute distance-dependent properties using Chemfiles, PDBTools, etc.

m3g.github.io

Martínez Molecular Modeling Group

MCKin

Computes using a MC simulation the mean first-passage times between every pair of reaction coordinates, given a PMF

mdanalysis

MDLovoFit

MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular Dynamics simulations. It allows the automatic identification of rigid and mobile regions of protein structures.