[gmx-users] Minimisation

[Justin Lemkul]

On 5/22/17 6:47 AM, Pandya, Akash wrote:
> Hi all,
>
>
> During Minimisation I get the following output that the simulation ended prematurely.
>
>
>
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =       500000
> Step=    0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax=         inf, atom= 6640
> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax=         inf, atom= 6640
>
> 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)
>
> How do I increase my constraint accuracy? Which file do I have to change?
>

That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-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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