Adwaita Nair

4 Questions 6 Answers 0 Followers

Questions related from Adwaita Nair

What is the initial atomic velocity assigned (by default) in GROMACS for simulation of protein ?

I have run a 100ns simulation run of my protein, but I would like to know about the initial atomic velocity that is assigned. Below is the md.mdp file that was available from the GROMACS tutorial...

20 December 2023 4,679 2 View

What could be the possible reasons for high PDI value (~0.7) of gold nanoparticle which was observed through DLS ?

The gold nanoparticle was synthesised through Turkevich method. And also kindly suggest ways to work towards lowering the PDI index.

16 April 2023 8,609 1 View

How to plot 3D free energy landscape ?

After using the command: gmx sham -f PCAplot2d.xvg -notime -ls gibbs1-2.xpm (where PCAplot2d.xvg is the PCA plot generated with the gmx anaeig command) I get the matrix file in a 2D plot, which...

08 December 2022 5,748 0 View

Bioinformatics tool for finding salt bridges and hydrogen bond in a protein structure ?

Could anyone suggest any web server/software/ any other method which identifies or lists all the salt bridges and hydrogen bonds present in a protein structure.

06 November 2022 7,703 2 View