Dear all lammps users,
I’m measuring the diffusion coefficient of lipid molecules in a vesicle. The command that most fits my purpose is compute msd/chunk. And chunk is defined as a group of lipid molecules. But issue is that compute msd/chunk calculates and prints out the msd of each molecule individually at each iteration. For measure of diffusion coefficient of lipids in vesicle, it needs to be long iteration(at least one million iterations). Therefore, it will limit the the number of molecules in the chunk, otherwise the msd file generated will be too large for post processing ( I need to get average msd of molecules at each step). Currently, the largest number of molecules possible in the chunk are 100. But, the msd vs time are are not linear, which means either I need longer iterations or larger numbers of molecules. But, it is not feasible to increase either. Is there alternative to do this, such as averaging the msd of molecules automatically like old command compute msd/mol do ? I know compute msd is not a good idea. Below is the command I used.
group mole molecule <= 50
compute molechunk mole chunk/atom molecule
compute 2 all msd/chunk molechunk
Thank you
Best,
Sean