Vijay Manickam Achari

13 Questions 25 Answers 0 Followers

Questions related from Vijay Manickam Achari

Is calculation of water diffusion in MD done in 2D or 3D?

I am trying to calculate the water diffusion in a hydrated bilayer system. Here I wish to know if the water diffusion normally calculated in 2D (x-y)or 3D (x-y-z)? Hope I get some insight on...

02 February 2015 7,281 2 View

We do my DFT calculations on sugar+lipid systems give CPHF error?

I am doing DFT calculation on sugar lipid system. The command I used is "#n opt freq=noraman b3lyp/6-311++g(d,p) geom=connectivity scf=qc". I get error message as below: LinEq1: Iter=992 NonCon= 1...

01 January 2015 8,554 7 View

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...

08 August 2014 2,755 2 View

How can I determine bilayer thickness and d-spacing from simulation?

I would like to determine bilayer repeat distance (d-spacing) from a simulation of a bilayer in water. This bilayer has water layer at the top. Followed by two monolayers and another single water...

07 July 2014 710 4 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...

07 July 2014 2,066 10 View

How do you find the average vector for lipids in bilayers?

I have simulated a lipid bilayer. The trajectory has about 20000 frames. Each frame contains 128 lipids where 64 lipids reside in the upper layer and the rest in the lower layer. I want to...

06 June 2014 6,888 4 View

Any suggestions for finding fitting function?

I am trying to fit a correlation function as attached in this post. Normally, single exponent function is used to fit the function. Since this plot has negative range, single exponent function...

12 December 2013 6,914 17 View

Can anyone advise on a model for atomistic simulation with a water layer in between two bilayers?

Recently, I had an idea to simulate hydrated bilayers. The model that I am interested on is a double bilayer with a water layer in-between the bilayers. Something like (bilayer-water-bilayer). I...

11 November 2013 5,776 5 View

Can anyone help with anisotropic and semi-anisotropic pressure couplings?

In literature, there are some bilayer simulation work apply anisotropic pressure couplings. Whereas, some use semi-anisotropic pressure couplings. Technically I know what these pressure couplings...

11 November 2013 2,858 1 View

I would like to know the meaning of "axial diffusion" of lipids in membrane bilayer?

Lipids in membrane bilayer do exhibit few types of motion, e.g: rotational motion, translation motion, vibration and so on. But I am quite unsure how the motion would like to be for axial diffusion.

09 September 2013 3,890 5 View

Does anyone gave experience with auto correlation function plot giving negative values?

I am simulating a bilayer and intend to calculate some dynamical properties. I tried to calculate the relaxation time for the chains in the hydrophobic region. For this I choose a vector along the...

07 July 2013 1,068 2 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...

05 May 2013 1,798 12 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,...

03 March 2013 1,019 1 View