Baibhabshri Roy

4 Questions 3 Answers 0 Followers

Questions related from Baibhabshri Roy

How to explain the plot from gmx clustsize?

I am doing md simulation for protein aggregation. For doing cluster analysis I was trying with gmx clustsize. Now the plot that I am getting, can not find a proper explanation. With -hc flag the...

25 June 2024 5,198 0 View

How to perform Brownian dynamics simulation with gromacs?

I want to study the protein aggregation of two different protein, one monomer and another fibril having 5 chains. I want to use coarse-grained model. Is it possible to use brownian dynamics with...

07 March 2024 3,301 2 View

Protein is going out of the water box in gromacs 2019.6

Hi, I am doing simulation of 2 proteins, one is a protein fibril having 5 chains and another is the unfolded monomer, there are total 740 residues. After nvt equillibration the protein is going...

01 January 1970 5,895 2 View

Coarse-grained md simulation with gromacs

I have a doubt for coarse grained md simulation. I have used martinize.py script to model the protein. But from here I do not understand on what basis it modelled the protein. There are 2 chain in...

01 January 1970 9,762 1 View