[gmx-users] query regarding center of mass removal

[Justin Lemkul]

On 1/3/20 3:29 PM, Snehasis Chatterjee wrote:
> 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.

For any system in an isotropic medium (i.e. water), comm-grps should be 
set to "system" because there are not multiple phases that may diffuse 
differently. You shouldn't use Protein/Non-Protein here; that's for tc-grps.

-Justin

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Justin A. Lemkul, Ph.D.
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