[gmx-users] metal ions in equilibration step

[Justin Lemkul]

On 6/6/17 8:22 AM, Mahboobeh Eslami wrote:
> Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step,  should I consider protein,ligand and calcium ions as one single entity (for tc_grps option)? or should I consider these calcium as the part of ions in sol-ions group?ThanksBest
> 

I consider structural ions to be part of the protein, not part of the bulk solution.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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