#molecular-dynamics

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

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 it proper topology and structure information.

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 a coarse-grained lipid system. In

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 structures. But on running it for a longer

Hello friends... Welcome to my new molecular dynamics post. As I mentioned in my previous post, I am going to start the new series on coarse-grained lipid models. As an opening article to this series,

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 the results in the form of HIVE blogs(under

Hi friends... To be honest I am overwhelmed with many things recently. And few days back my tinkering became official work(Well... Kinda). Few of you might have seen my previous post. So I will elaborate

This is a reproduction of the Hongyan Yuan et al paper "One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes".The simulation was done in LAMMPS and the parameter

![]( Hello Friends! Our new paper got accepted. It's my second paper. The link to the paper is below: Unfortunately, it is behind the SPRINGER paywall! I should write a summary of the paper soon here at

In my previous articles, we have seen many examples which demonstrated classical molecular dynamics simulations of bigger systems likeProtein complex in water boxA lipid bilayer patch system in water

The day after tomorrow, the Free energy calculations for chemical and biological systems workshopwill begin at IIT, Kanpur. I have got selected for it! And I am very excited to learn new stuff

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 lipids which specifically exhibit this

Recently we did some all-atom classical molecular dynamics simulations involving DMPC model membrane, Nogo66 membrane active protein, TIP3P water model and NaCl ions. We used CHARMM36 forcefield and ran

Below is a youtube video of 50 nanoseconds long trajectory of a recent all-atom molecular dynamics simulation which I did using NAMD software. The yellow dots are sodium ions and cyan dots are chloride

Below is a video of two 400ns long all-atom classical molecular dynamics trajectories of Rap:Raf complex. The "ice blue" and "orange" tubes are Rap:Raf complex with phosphorylated Serine

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, see the figure below: A typical correlation

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 promotes binding affinity of Rap-Raf

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 few months. This is about my first research

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 plots based on the density of scatter

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