[gmx-users] COM removal
senthilk at engin.umich.edu
Tue Jul 22 19:38:01 CEST 2003
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?
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