[gmx-users] COM removal

[Senthil Kandasamy]

Hi all,

I am not sure if I understand correctly what COM removal does. The 
following is  my understanding.

When I do not apply COM removal to the system, the system gains a net 
momentum due to truncation errors and the box starts drifting. To prevent 
this from happening, COM removal can be applied to the entire system. This 
does some sort of rescaling to prevent the box from moving. However, when I 
start applying COM removal to individual groups, doesn't this affect the 
true dynamics  of the system? If I need to calculate diffusion coefficients 
of  a particular group (Say group AAA)  then I can still do this 
calculation if Comm-grps = system was chosen, but not when comm-grps = AAA .

Am I correct ?

I need to calculate diffusion coefficients of some peptides at lipid/water 
interfaces, but have used COMM removal on the peptides, lipids and SOL 
separately rather than the whole system. I think I need to rerun these 
simulations. Don't I?

Senthil