Ali Ghamartale

2 Questions 17 Answers 0 Followers

Questions related from Ali Ghamartale

How does the gmx rdf will act if we consider multiple molecules for -ref?

I need to calculate the radial distribution function for my system which includes 50 molecules. Here is my code line to generate rdf in gromacs: gmx rdf -n Index.ndx -f mdrun1.xtc -s mdrun1.tpr...

05 January 2021 5,126 8 View

How to measure angle between two types of molecules with "gmx gangle" in GROMACS?

I have a box let's say full of toluene, I want to measure the angle between toluene molecules versus distance. I think I should use "gmx gangle"; however I am a bit confused about how to select my...

21 December 2020 8,579 4 View