[gmx-users] query regarding center of mass removal

[Justin Lemkul]

On 1/4/20 1:38 AM, Snehasis Chatterjee wrote:
> Thank you Prof. Lemkul for your kind reply. In mdp file, I will set
> comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions?
> 240 Ca2+ ions are non-covalently attached with the capsid and have
> important role in maintaining capsid stability.
>
> I am also planing to run another set of simulation, where RNA is
> non-covalently attached with the capsid. In tc-grps, I can couple capsid,
> RNA and Ca2+ ions together. I am looking forward for your reply.

Generally solute and solvent are coupled separately, however you define 
what the solute is.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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