Eugene's Science Archive

@UC20w93QLpQ3FTbbXWBKRJhA - 80 subscribers

Hello, my name is Eugene! I created this channel to share my experience in science (mostly, scientific computing). My fields of scientific interest include in vitro cultivation of plants and fungies, studying impact of biologically active substances on morphology and physiology on plants and fungies at organismal and cellular levels, structural bioinformatics (this will probably be main content of the channel). Occasionaly, I also program (Python, C++, Rust) and compile stuff, so if you are into this and my way of doing things - welcome! As of autumn 2025, I have finally defended my PhD degree in biology.

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Predicting protein-ligand complex using Protenix Server

Predicting protein-ligand complex using Protenix Server Eugene's Science Archive

5 views - 2 days ago

$How to use gmx check of GROMACS package to find errors in\compare your simulation files data$ 8:34

How to use gmx check of GROMACS package to find errors in\compare your simulation files data Eugene's Science Archive

27 views - 1 week ago

Extracting general info about system and simulation with gmx report-methods tool of GROMACS package

Extracting general info about system and simulation with gmx report-methods tool of GROMACS package Eugene's Science Archive

9 views - 2 weeks ago

Mean Squared Displacement (MSD) with GROMACS

Mean Squared Displacement (MSD) with GROMACS Eugene's Science Archive

52 views - 3 weeks ago

Dumping GROMACS files to extract technical data

Dumping GROMACS files to extract technical data Eugene's Science Archive

46 views - 4 weeks ago

Distance calculations with gmx mindist

Distance calculations with gmx mindist Eugene's Science Archive

33 views - 4 weeks ago

Defining secondary structure with GROMACS

Defining secondary structure with GROMACS Eugene's Science Archive

42 views - 4 weeks ago

Ramachandran plots with GROMACS

Ramachandran plots with GROMACS Eugene's Science Archive

75 views - 4 weeks ago

Distance calculations with gmx distance program

Distance calculations with gmx distance program Eugene's Science Archive

65 views - 4 weeks ago

Salt bridges calculations using VMD with GROMACS trajectories

Salt bridges calculations using VMD with GROMACS trajectories Eugene's Science Archive

23 views - 1 month ago

Loading GROMACS trajectory into VMD: file input, molecular representations, animation

Loading GROMACS trajectory into VMD: file input, molecular representations, animation Eugene's Science Archive

153 views - 1 month ago

Principal Components Analysis (PCA) with GROMACS package. Part II: more 3D output

Principal Components Analysis (PCA) with GROMACS package. Part II: more 3D output Eugene's Science Archive

39 views - 1 month ago

BFS/CIP approach for R/S chiral center detection in molecular structures implemented in Rust

BFS/CIP approach for R/S chiral center detection in molecular structures implemented in Rust Eugene's Science Archive

20 views - 1 month ago

Principal Components Analysis (PCA) with GROMACS package. Part I: tools & basic output

Principal Components Analysis (PCA) with GROMACS package. Part I: tools & basic output Eugene's Science Archive

192 views - 3 months ago

SASA calculations with gmx sasa program

SASA calculations with gmx sasa program Eugene's Science Archive

91 views - 3 months ago

Gyration calculations with gmx gyrate-legacy program

Gyration calculations with gmx gyrate-legacy program Eugene's Science Archive

33 views - 3 months ago

Gyration calculations with gmx gyrate program

Gyration calculations with gmx gyrate program Eugene's Science Archive

24 views - 3 months ago

RMSF calculations with gmx rmsf program

RMSF calculations with gmx rmsf program Eugene's Science Archive

82 views - 4 months ago

Hydrogen bonds calculations with gmx hbond-legacy tool (gmx hbond before 2024)

Hydrogen bonds calculations with gmx hbond-legacy tool (gmx hbond before 2024) Eugene's Science Archive

34 views - 4 months ago

Hydrogen bonds calculations with modern gmx hbond tool

Hydrogen bonds calculations with modern gmx hbond tool Eugene's Science Archive

75 views - 4 months ago

RMSD calculations with gmx rms program

RMSD calculations with gmx rms program Eugene's Science Archive

131 views - 4 months ago

Static build of MOPAC v. 23.2 on Fedora Linux + running resulting MOPAC executable on WSL2 Ubuntu

Static build of MOPAC v. 23.2 on Fedora Linux + running resulting MOPAC executable on WSL2 Ubuntu Eugene's Science Archive

156 views - 4 months ago

Installing CMake v. 4.1.1 from source code on Fedora Linux

Installing CMake v. 4.1.1 from source code on Fedora Linux Eugene's Science Archive

58 views - 5 months ago

Installing GROMACS 2025.3 from source code on Fedora Linux

Installing GROMACS 2025.3 from source code on Fedora Linux Eugene's Science Archive

70 views - 5 months ago

Index group operations with gmx make_ndx tool

Index group operations with gmx make_ndx tool Eugene's Science Archive

110 views - 5 months ago

How to install and use gmx_MMPBSA tool v. 1.6.4 to determine binding energy of complex after MD

How to install and use gmx_MMPBSA tool v. 1.6.4 to determine binding energy of complex after MD Eugene's Science Archive

286 views - 5 months ago

Performing cluster analysis using gmx cluster - GROMACS 2025.2

Performing cluster analysis using gmx cluster - GROMACS 2025.2 Eugene's Science Archive

329 views - 6 months ago

Basic molecular dynamics trajectory operations with gmx trjconv - GROMACS 2025.2

Basic molecular dynamics trajectory operations with gmx trjconv - GROMACS 2025.2 Eugene's Science Archive

296 views - 6 months ago

How to stop/continue/extend simulation with gmx convert-tpr - GROMACS 2025.2

How to stop/continue/extend simulation with gmx convert-tpr - GROMACS 2025.2 Eugene's Science Archive

198 views - 6 months ago

Molecular dynamics simulations of multiple proteins and ligands - GROMACS 2025.2

Molecular dynamics simulations of multiple proteins and ligands - GROMACS 2025.2 Eugene's Science Archive

178 views - 6 months ago

Predicting protein heterodimer using AlphaFold Server

Predicting protein heterodimer using AlphaFold Server Eugene's Science Archive

91 views - 6 months ago

Installing GROMACS 2025.2 from source code on WSL2 Ubuntu

Installing GROMACS 2025.2 from source code on WSL2 Ubuntu Eugene's Science Archive

217 views - 7 months ago