Cneter of mass one molecule?

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Hi everyone

How can I determine the center of mass of a molecule during an MD simulation and identify the specific atom that represents this center?

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You can calculate the centre of mass of whatever is in your system by using, for example, the command gmx traj and specifying the flag -com. Most likely, you will also have to specify the molecule in the index file (add the flag -n and point to an index file that contains the group defining the molecule).

My understanding is that the centre of mass is just a vector, that is, an (x,y,z) position in the box, but it does not correspond to anything, e.g. an atom. However, if you have a molecule with some kind of rigidity where you expect the centre of mass to be relatively constant within the reference system centred in your molecule, you can look for which is the nearest atom to that (x,y,z) position and see if the centre of mass ¨falls" on top of this atom.

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In the context of molecular dynamics (MD) simulations, the ‘center of mass’ (COM) refers to the average position of the masses of all the atoms in a molecule. It is a useful quantity for characterizing the overall motion and behavior of a molecular system. You may be interested in the motion or behavior of a specific residue, ligand, or functional group within the molecule. In this case, you would calculate the center of mass for that particular subset of atoms.
For more information : https://manual.gromacs.org/current/onlinehelp/gmx-traj.html

4

Thank you for your respons. Honestly, I’m aiming to calculate the Mean Squared Displacement (MSD) for specific one single molecule during the molecular dynamics (MD) simulation. I’ve tried using both gmx msd and gmx msd -mol , but the resulting values for MSD are quite different. I’m not sure if it’s really necessary to calculate the Center of Mass (COM) MSD for just one molecule. oor i can used gmx msd without -mol flag…Any thoughts or advice on this?

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thanks you…according to your response
If I aim to calculate the Mean Squared Displacement (MSD) of a particular molecule and study its motion behavior, would it be essential to use the Center of Mass (COM) for this analysis?

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Please read the details here: https://manual.gromacs.org/current/onlinehelp/gmx-msd.html

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Check out: On the in silico application of the center-of-mass distance method