Dear all
I am involved in a project where the target systems are lipid bilayers
with and without different macromolecules embedded. In the past I did
quite a lot of MD simulations of membrane systems always removing the
COM motion of lipids and the solvent in separate groups. There are
several discussions about this in the gmx users list (see for instance:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108590.html)
but I do not understand clearly the reason to do this. I am very
interesting in determining diffusion coefficients, so the right removal
of COM is key for my analysis. Can anyone explain why the global removal
of COM for all the system might produce a lateral relative displacement
of the bilayer with respect to the solvent in opposite directions (thus
keeping the COM)? Is it guaranteed that this is solved by removing the
COM separately for lipids and the solvent? When I have macromolecules
embedded in the membrane, should I remove the COM of the macromolecules
together with the lipids?
Thank you in advance for any help,
Ángel.
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