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

Erik Marklund erik.marklund at kemi.uu.se
Tue Sep 27 09:31:13 CEST 2016

> On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acharya at gmail.com> wrote:
> Dear Gromacs users,
> I am trying to perform a simulations of different concentration of peptides
> in a box with lipid bilayer. In this context, I had a query regarding the
> correct Center-of-Mass removal settings; what would be the correct way to
> ensure that the Membrane is stationary during long simulations while the
> peptides, solutes etc freely diffuse in the box. Based on my understanding,
> I am using the following settings in the parameter file:
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = MEMB SOL_ION Peptide
> Here the Peptide group includes a total of say 16 peptides. Would this be
> the correct way to perform the simulation?
> Is is possible to set individual nstcomm values for each group so as to
> ensure that the peptides diffuse freely while the membrane stays stationary?

Why do you want that in the first place? Membranes aren’t stationary.

Kind regards,

> The full mdp settings I intend to use is provided in the following link:
> https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00/view?usp=sharing
> Please advise of what would be the best settings to perform the simulation.
> Best Regards,
> Abhishek Acharya
> Bangalore.
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