Ashutosh Anand

4 Questions 3 Answers 0 Followers

Questions related from Ashutosh Anand

Why the water box is changing shape in NVT simulation?

I performed a minimization simulation of a water box using the tip3p water model in NAMD. The water box was in a sphere of radius 20nm and sphericalBCk1 of 10. The water box changed its shape from...

24 June 2021 9,896 2 View

How to simulate water droplet in a cavity using NAMD?

I do not know how to make a cavity in NAMD and simulate water molecules. What are the steps I should follow?

19 June 2021 3,465 6 View

How to visualize protein-protein interaction using PyMol?

I have a protein-protein docked complex and want to see the interaction between them using PyMol. What is the procedure to do so?

05 January 2021 6,846 2 View

Is energy minimization of a protein necessary?

I have modelled a protein structure, using Modeller software, which I will use for docking purposes. Is energy minimization necessary in this case?

30 December 2020 4,485 3 View