[gmx-users] COM removal
lindahl at stanford.edu
Tue Jul 22 20:30:01 CEST 2003
> 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
Correct. It's not really a scaling, though: you just remove the net
velocity of the system.
> 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 ?
Yes, partly. The whole idea with COM-removal is to compensate for
non-physical artefacts in simulations.
The most obviuous problem is that in contrast to the real world,
nothing stops your box from moving in space.
> 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?
For lipid bilayers it's a good idea to remove COM separately for the
water, upper layer and lower layer, since the lipid layers can show
non-physical diffusion against each other in the XY-plane.
If you apply COM to the peptide, it won't be able to move relative to
the water or lipids.
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