Arunabh Athreya

4 Questions 17 Answers 0 Followers

Questions related from Arunabh Athreya

How to make a HMMM bilayer through gromacs?

Hi I have been trying to make a HMMM bilayer through CHARMM-GUI but since the protein of interest is a well spread one, with certain domains being intrinsically disordered, I had to make a box 20...

18 September 2021 4,921 2 View

What's the expected free energy change in conformational transition of a transporter?

Hi I have been trying to optimize well-tempered metadynamics simulation in Gromacs 2020.4 engine using plumed, on a transporter from Major Facilitator Superfamily. I have the existing structure...

22 May 2021 3,766 2 View

PME or Reaction-field-zero for ionic interactions mediated protein conformational changes in Gromacs?

I am trying to assess change in protein conformation as a result of possible salt bridge formation and a couple of polar interactions. I wanted to know if using particle-mesh-Ewald electrostatics...

15 May 2020 8,311 0 View

What is sequence of origin of replication needed in a plasmid to propogate in Staphylococcus aureus or staphylococcus epidermidis?

Can a plasmid that expresses in Staphylococcus aureus also express in Staphylococcus epidermidis? Also, what are the common vectors used in S. epidermidis for protein expression?

24 November 2017 3,394 1 View