[gmx-users] Azurin protein attached to metal atom of Cu.

[Nicola Staffolani]

> How are you treating the bonds during the simulation?  If you're using
> "constraints = all-bonds," then this is precisely the outcome you should
> expect; all the requested bonds are indeed present and are being kept fully
> rigid by the constraint algorithm.  If there were no bond(s) produced by
> specbond.dat, then these distances would not be constant.
>
>
​which means that ​one should set "constraints = none" during the dynamics?

-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 601
> 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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-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36