[gmx-users] comm-mode option for applied external electric field.

ARNAB MUKHERJEE arnabmukherjee249 at gmail.com
Fri Feb 1 17:46:36 CET 2019


I am trying to understand the comm-mode option in .mdp. I am simulating a
DNA protein system with electric field. Now, if I understand correctly the
comm-mode option, if I set it to linear, and comm-grps to System, it will
remove the velocity of COM velocity of the system. But here I want to
compute the velocity of COM of protein (which is positively charged and
moves in the direction of the applied field). Here I am using Langevin
dynamics. So my question here is comm-mode option, as it removes the
velocity of COM, does it also rescale the coordinates? If I run the same
simulation by using the option comm-mode = Linear, and for other case
comm-mode = None, in these 2 cases I should get different trajectories,

Also, since for my case the protein and ions are driven by the field, I set
comm-grps = DNA_W, which is the group containing all DNA and water atoms
(here the DNA is position restrained). Is this the right thing to do here?
Or should I use comm-grps = none? I am confused here.

I would highly appreciate any help!

Thank you in advance.



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