[gmx-users] Hydroxyl bonds rotating too much

[Justin Lemkul]

On 5/16/17 7:03 AM, Juan José Galano Frutos wrote:
> Hi there:
>
> I am simulating a protein which include as a cofactor a molecule bearing
> some hydroxyl groups. The system is crashing from the begining of the
> equilibration step (after the following steps: vaccuum minimization,
> solvating, neutralizing, minimization, heating) due to -in all the
> replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
> degrees.
> I checked the structures and the systems looking for either water or
> protein parts in so close contact with this hydroxyl groups, but it was not
> the case. Then I proceeded to re-minimize again the systems after the
> heating step and afterward to relaunch the equilibration step, but again
> the same happened. I also checked the topology file of this cofactor but
> all seems to be fine, I mean charges.
> Then, what could be happening? Is it common this behaviour in hydroxyl
> groups?Any help please....
>

What does the problematic OH group interact with?  The over-rotation is a 
symptom, not a cause.  If it interacts with your cofactor, the parameters for 
that cofactor are likely suspect.  Typical diagnostic steps are in 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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