[gmx-users] LINCS warning

[Justin Lemkul]

On 8/25/16 5:56 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello users,
> I was trying to energy minimize my system of protein embedded in bilayer.
> But I am receiving the following error:
>
> Step -1, time -0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000942, max 0.149038 (between atoms 21616 and 21619)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =       500000
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 11 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  2.3557852e+30
> Maximum force     =            inf on atom 34347
> Norm of force     =            inf
>
> what approach should I use to get rid of this problem?
>

Infinite force most likely means you have atoms on top of each other.  mdrun 
tells you where the (first) problem is - atom 34347.  Inspect that area visually 
and figure out what part of your system preparation went wrong.

-Justin

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

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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