i want to find center of mass coordinate of the protein,for that i using the following command
gmx_mpi traj -f md_noPBC.xtc -s md.tpr -com -ox com.xvg -pbc
but i m not getting satisfactory results. what could be the issue .is it with this command or anything else
Do you select the protein as the reference group for the calculation when you use that command? What do you mean with "not satisfactory"? With respect to what?
yes i did select proteins
satisfactory mean its coming out to be fluctuating
Sorry, but shouldn't it be fluctuating? It's a simulation of the dynamics of the system, the protein is going to move around in the box.
Hi Manoj Rana,
Why do you need to select the center of mass (COM) of a protein? For example, do you want to determine the distance between the COM of the protein and a specific residue or a ligand?
You can use the "-seltype" and "-select" options in the analysis command.
Good luck