[gmx-users] mdrun error

[Justin Lemkul]

On 8/24/14, 5:28 AM, Lovika Moudgil wrote:
> Hi everyone ,
>
> Need some help .I have got an error in my mdrun . Upto grompp every thing
> was fine but when I give command for mdrun ,It stops with this ...
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        10000
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.08534e+18 Fmax=         inf, atom= 19
> 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 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  2.0853354e+18
> Maximum force     =            inf on atom 19
> Norm of force     =  1.7429674e+18
>
> constraints are all ready none ...Please help me what should I do to solve
> this .

You have an infinite force, so that means severe atomic clashes or a totally 
distorted geometry.  mdrun tells you atom 19 is in the neighborhood of the 
problem, so visualize and see.

-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

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