[gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Erik Marklund erik.marklund at kemi.uu.se
Thu Sep 29 11:05:18 CEST 2016


I don’t simulate membranes much, so perhaps someone else’s input might be more valuable. But unless the relative motion of the membrane with respect to the rest is artificial and not just diffusion, I would still recommend COM-motion removal of the whole system.

Kind regards,

> On 28 Sep 2016, at 16:39, Abhi Acharya <abhi117acharya at gmail.com> wrote:
> Thank you Eric for your clarification. However, I have seen that in
> membrane simulations, its is suggested to couple membrane, and solvent and
> solute to two different COM groups. The argument is that in case of
> membrane systems, there is an inherent tendency of lateral drift of
> membranes; with a single COM for the whole system, even though the COM
> would remain essentially unchanged, there may be appreciable drift of the
> membrane relative to the rest of the system. Could you possibly shed some
> light on this?
> Following the above argument, probably for my system I should assign
> membrane to one COM group and the rest of the system (including solute
> solvent and the peprides ) to other. What do you think?
> Thank you.
> Regards,
> Abhishek Acharya
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