I have a coarse-grain molecular dynamic performed in Gromacs. I am interested, in computing the distance between an atom (bead) and a group of atoms (beads). That is to say, I want the distance from a particular bead of my membrane protein to the last beads of the lipids chains (this is the center of the membrane). All the lipids have the same bead at the final of the chain.
Please, any suggestions?
First of all, there is nothing like "the distance", but instead "a distance". There are many distances. For instance Euclidean sqrt( sum on i =1 to N of (y(i)-x(i))**2)
But also sum on i=1 to N of |y(i)-x(i)|, and you have many more, like the taxi-cab or Minkowski/Manhattan distance.
The only requirement for a distance is that distance from a to b + distance from b to c is superior or equal to distance of a to c, with other obvious requirements (d(a,b)=0 implies a=b, the distance has to always be positive or zero).
You may want to compute A DISTANCE between the centroid of a group of atoms and another one. Then how do you define this centroid? Mass center probably...
Does this help you?
Thank you very much, Professor Renaud Di Francesco.
Certainly, Gromacs allows generating an index with groups. In my case, one group contains only one bead and the other group contains each final bead of the lipids that compose my membrane lipid. With this array, I could compute a distance between them using the center of mass. I only have the doubt of whether this is valid for a system as dynamic as lipid membranes.
https://www.sciencedirect.com/topics/engineering/coarse-grained-molecular-dynamic
https://www.sciencedirect.com/topics/materials-science/coarse-grained-model
Check https://www.sciencedirect.com/topics/engineering/coarse-grained-molecular-dynamic
Also check https://aip.scitation.org/doi/am-pdf/10.1063/1.4898625
Hello Akiko,
You can use this
https://www.sciencedirect.com/topics/materials-science/coarse-grained-model
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