computational-biophysics Tag Posts Index

COOKE-DESERNO membrane patch forming cylinder!

This is a simulation I am currently doing. The model is described here:

Creating a CG vesicle structure and coordinate file for simulations

Hello friends! I am back with my coarse-grained(CG) molecular dynamics(MD) simulation series. Today we will see how to create a vesicle coordinate file and assign

Coarse-grained simulation of lipid vesicles using Farago model

See my recent article for the model. This is an attempt to see if I can see the fusion event between two vesicles. Will report the results once I finish the entire

Modelling a "water-free" coarse-grained lipid system

In the last article, we saw how to set-up a coarse-grained simulation using LAMMPS software. In today's article, I will discuss how to come up with a model to simulate

Longer run of the LAMMPS code from previous post exhibits bilayer self assembly !

I just wanted to update you guys with a longer run of LAMMPS code in my previous article. In my previous article, it seemed that we were observing micelle like

A discord server for Biophysics learning and discussions!

Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document

Tracking Interdigitated lipids from MD simulations

When using softwares like VMD to visualize membranes where lipids exhibit interdigitation as in our case, it will very useful if you can sort out those

Visualizing Lipid Defects in model membrane simulations

Recently we did some all-atom classical molecular dynamics simulations involving DMPC model membrane, Nogo66 membrane active protein, TIP3P water model and NaCl

Understanding Correlation measurements of Protein motions from MD trajectories

Today let us try understanding correlation maps. It is very common to see correlation maps of protein motions in molecular dynamics research papers. For example,

Why SER11 site was chosen as the phosphorylation site? : A frequent question which we encounter regarding our work

Hi friends... Recently I had written about our research work which got published in this August. Those who have not read that article can find it below: Phosphorylation

Phosphorylation promotes binding affinity of Rap-Raf complex [Original Research Work Summary]

Hello, my dear friends! Welcome to yet another science article from @dexterdev. Today I am going to write about something which I was thinking to do for the last

Addendum to my previous post: PCA caveat + Tracking Ubiquitin in the Principal component space

This is an addendum to my previous post which you can see here: Repository PCA caveat From PCA plots it is possible to create normalized histograms or distribution

Studying fluctuations in proteins from Molecular Dynamics trajectories

Hi friends... Welcome to yet another article from @dexterdev. Molecules are not stationary entities. Most of the molecules function via dancing in particular patterns.

How to create infinite structures for Molecular Dynamics simulations?

Hello, my dear friends! @dexterdev is back after a long gap. Today I will discuss on creating infinite molecular structures for MD simulations!!! (Sounds impossible