[gmx-users] query regarding center of mass removal

[Snehasis Chatterjee]

Dear Gromacs users,

I am trying to perform a virus capsid simulation using GROMACS 2018. 240
Calcium ions bound to specific regions of the capsid and have important
role in maintaining capsid stability. In this context, I had a query
regarding the correct Center-of-Mass removal settings. I usually run
protein simulation in aqueous environment using following mdp options:



*nstcomm= 100comm_mode= linearcomm_grps= Protein Non-Protein*

In aqueous environment, I typically use "Protein Non-Protein," with
Non-Protein containing solvent and ions. Since, 240 Ca2+ ions are
non-covalently attached with the capsid, I am planing to couple  capsid
with Ca2+ ions. I am bit confused regarding this issue. Any kind of advice/
suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee