I want to compute MSD for about 20 polymeric (~40 mers) units over time. I have two questions.
- Does compute MSD command computes the MSD for each polymer molecule seperately and print outs their average or does it compute the MSD of all the atoms as one entity?
- In addition, how do we make sure that these diffusion is not baised by any overall translation or rotation of the system? Through “com” option in compute msd or through fix momentum command.
- Based on the doc page, am I correct to say that we can use restart file (with all specified assigned fixes) to continue a longer trajectory if needed without any problem?