Hi, 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, right?
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. Regards, Arnab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.