[gmx-users] Non-neutral system with iron-sulfur clusters

[Justin Lemkul]

On 6/14/16 4:59 AM, Marlon Sidore wrote:
> Hello everyone,
>
> On my quest to use the parameters for iron-sulfur clusters from [1] I
> realized that the resulting clusters are not neutral. Indeed, even though
> the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
> of the cluster + the 4 CYS isn't a round number.
>
> Should I worry ?
>

Non-integer charges are totally non-physical, so using such a topology would be 
wrong.  Check carefully that you've assigned everything correctly.

-Justin

> 1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
> C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J.
> Chem. Theory Comput. 8, 2103–2114 (2012).
>
> Marlon Sidore
>
>
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
>

-- 
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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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