Erma Fatiha Muhammad

4 Questions 4 Answers 0 Followers

Questions related from Erma Fatiha Muhammad

How to solve Hbonanza error ?

Hi everyone. I want to use hbonanza to analyses hydrogen bonds formation during MD simulation time for my protein-ligand complex system. Previously, I run md using GROMACS 4.6.5, further, I try to...

03 March 2015 290 3 View

Could it be NVT ensembles followed by NPT ensembles during the molecular dynamics simulation?

1. I have used many ways in order to prove the stability of my conformation system. One of the way is to use equilibration using canonical ensembles (NVT) followed by isothermal isobaric ensembles...

11 November 2014 5,634 6 View

Is it correct to use PRODRG beta server to create a topology file for use in Molecular dynamics simulation?

I am doing the molecular docking and molecular dynamics simulation of protein-ligand interactions. In the first part, I was doing blind docking to find the possible binding sites between protein...

11 November 2014 8,898 3 View

What analyses can be done to investigate the "dynamic behaviour" of protein after molecular dynamics simulation by using Gromacs software?

molecular dynamics simulation

10 October 2014 3,703 6 View