[gmx-users] removal of center of mass motion needed for accelerated water molecules?

[Yang Wang]

Hi all,

I have a periodical system comprised a nanotube and water solvent. Positive
acceleration is applied to every water molecules and I am trying to count
the water flux through the nanotube. I also specified force constraints
(1000) on the nanotube to keep it in place. The question is whether removal
of center of mass motion is needed for this kind system with accelerated
water molecules. I performed the simulation with removal of center of mass
motion for the nanotube and water as two groups (nstcomm=1,
comm-mode=Linear, comm-grps=CNT SOL).The flux result is significantly
smaller than the result from simulations w/o removal of center of mass
motion.

As I understand it, removal of center of mass motion is generally required
for equilibrium MD runs in Gromacs. However, the simulations that I
performed are non-equilibrium MD runs. Could anyone help me with some
advices on this problem? I highly appreciate your help!

Sincerely,

Yang

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