Everything Happens for a Reason

Recent posts

 

Download Protein Ensemble Database entries

IDP
The Protein Ensemble Database (PED) is a freely accessible repository designed for the submission of structural collections, which include intrinsically disordered proteins…
Oct 14, 2023
Quyen Vu

 

Extracting information from IDP database and IDP classification

IDP
PED
MobiDB
DisProt
Proteins are complex biomolecules crucial for the functioning of living organisms. They come in various shapes and sizes, each designed for specific functions within cells.…
Oct 1, 2023
Quyen Vu

 

All-Atom simulations of IDP

Research
IDP
LLPS
Galvanetto et al. (2023) used Amber99SBws force field with the TIP4P/2005s water model. Their FFs for Gromacs can be download from: https://github.com/bestlab/force_fields.…
Aug 17, 2023
Quyen Vu

 

Some Conda Commands Frequently Used

Python
conda is a great python package environment.
Feb 24, 2023
Quyen Vu

 

Simple OpenMM system for testing code development

OpenMM
This post contains a simple system definition of two beads with custom nonbonded for testing
Feb 9, 2023
Quyen Vu

COSMO tutorial

IDP
OpenMM
This tutorial guide you how to use cosmo package to perform coarse-grained simulations of IDPs
Feb 4, 2023
Quyen Vu

Implementation of Mpipi model in OpenMM

IDP
OpenMM
Mpipi model is a coarse-grain model for simulating IDP. The original code is implemented in LAMMPS but I am not familiar with LAMMPS either.
Jan 11, 2023
Quyen Vu

Make a beautiful plot using Matplotlib

Python
Visualization
When writing a paper, a beautiful figure is very important. Before, I used Gnuplot or XMGRACE to make figures because it is easy to config.
Dec 24, 2022
Quyen Vu

 

Problems regarding ipywidgets has no attribute ‘version_info’

Python
With the recent update of ipywidgets, Pyemma, MDAnalysis and some other package encounter problems with ipywidgets.
Dec 11, 2022
Quyen Vu

 

Some Linux commands frequently used

Linux
This post contains some bash code-snippet to make my daily work easier.
Dec 9, 2022
Quyen Vu

 

Openmm Coarse-grained Simulations

HPC
Slurm
OpenMM
Notes on cluster information:
Dec 9, 2022
Quyen Vu

 

Slurm scripts and commands to submit jobs on clusters

HPC
Slurm
To request for 1 node (-N 1), 8 threads and 8hrs
Nov 26, 2022
Quyen Vu

Amino acid table

Protein
21 amino acids make up proteins.
Nov 25, 2022
Quyen Vu
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