I am trying to run a NVT simulation using positions restraints using Gromacs 2020.5. I am holding a graphene sheet fixed in the x and z-axis. In my simulations, I am using Nose-Hoover thermostat.
However, I am having several warnings, and looking to the GROMACS forum I found several messages but I did not get what I really should do.
So, if I use position restraints I get the warning:
"Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible."
Them I am using comm-mode = None. From this “old” discussion Re: [gmx-users] com motion and position restraints may cause artifacts seems that NVT without center of mass remotion is OK.
However, with comm-mode = none, I get this warning:
"You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass"
So what I should do? Use or not use the center of mass removal?