Dear All users,
I want to convert my atomic trajectory file into COM(center of mass) trajectory. In fact I want to save the center of mass of my atoms in new trj file. How can I do this? does any one have some experiences in this area?
You can compute the COM for a group of atoms with a variable that uses
the xcm function, or via the compute com command. You can output
those quantities in various ways.
Steve
Dear Steve,
Thank you very much for your reply.
Yes, you are right. I used this command but I need more analysis of my outputs. I’ve recorded the COM’s coordinates every 1000000 steps and my total
time step is 1.2 million steps. Besides, I’ve gotten warnings which implies that my groups have atoms which do not belong to the groups while I have had very simple molecules
such as propane(all atom).