Analysis from output

User discussions
1

GROMACS version: 2020.4
GROMACS modification: Yes
Here post your question : I have a protein with 5 domains and a dsDNA . I want to calculate the angles and distances between centers of masses of the domains and DNA. Do I make indexes of all the domains from the output files of the simulation and then use gmx distance ? or this will be easier with MD analysis? A workflow would be highly appreciated.

2

Hi,
I understood that you what to calculate the distance between com of the DNA and com of each protein domain, then you can also use gmx pairdist see https://manual.gromacs.org/current/onlinehelp/gmx-pairdist.html
\Alessandra

3

Hi Madam, are the MD analysis scripts for angle between the domains and Center of mass more helpful in terms of plotting the data and working with them?