Vijay Manickam Achari

4 Questions 10 Answers 0 Followers

Questions related from Vijay Manickam Achari

What is the best method for calculating diffusion of lipids in bilayer via simulation?

I am trying to calculate lateral lipid diffusion via simulation in the xy direction . The method I used to calculate the diffusion is by calculating the gradient or slope of plot of MSD (mean...

13 August 2014 7,012 2 View

How can I calculate hydrogen bonding from simulation?

I would like to calculate Hydrogen Bonding (HB) interaction from simulation a simulation. Let's say I have two molecules (molecule A and molecule B) with several OH groups in each molecule. At...

10 July 2014 8,659 10 View

Calculating auto-correlation function from MD simulation?

I would like to calculate auto-correlation function for tilt angle for the lipids in a bilayer from molecular dynamic simulation. I have the angles for all lipids from each frames for all...

02 May 2013 2,979 11 View

How to determine the lipid-bilayer distance from small angle X-ray study and molecular dynamics simulation study.

In X-ray study, normally the bilayer repeat distance is determined (shown as D in this paper (Nagle, J.F. and S. Tristram-Nagle, Lipid bilayer structure. Current opinion in structural biology,...

23 March 2013 5,342 1 View