Calculate speed at which two groups move towards each other

User discussions
1

I’m wondering if there is a way to calculate the speed at which two groups (drugs and polymer) move towards each other?

Also, is there a way to calculate the number of contacts between the two groups during the simulation? Is there a ‘default’ contact distance?

Thanks!

2

Hi @kwaldner,

I am not sure about your first question. You could maybe calculate the velocity of the center of masses of the groups. But maybe somebody else can help you more on that point.

For the second question, I would suggest to calculate the RDF/CDF of the polymer around the drugs (or the other way around, depending on your interest). The advantage is that the RDF and the CDF cover a wider range of distances than a simple contact analysis with only one cut-off. If you really want/need an analysis of the contacts you could use the distance at the first minimum of the RDF as a cut-off value. GROMACS has implemented tools for both types of analysis → gmx rdf and gmx mindist.

Hope I could help you!
Marius

3

Thanks @Marius, that’s a good suggestion to use RDF. I will try that. Is there a straighforward way to calculate the velocity of the COMs?

4

Hi @kwaldner,

please take a look at this recent blog post:

Cheers,
Marius

5

What information you can get byt getting this value?