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

[Abhi Acharya]

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?

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
C-CAMP
Bangalore.