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

[Justin Lemkul]

On 4/30/14, 9:59 AM, Nicola Staffolani wrote:
>> 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?
>

If the fluctuations of the bonds are important to what you're doing, yes.  Also 
reduce dt as needed.

-Justin

-- 
==================================================

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

==================================================