[gmx-users] why minimization stop so fast

[Justin Lemkul]

On 4/16/13 1:05 PM, Albert wrote:
> Hello:
>
>   I've built a system with CHARMM-GUI, and I am trying to mimize it with
> following  em.mdp file
>
>
> title               = steepest descent energy minimization
> define              = -DPOSRES -DPOSRES_LIG
> cpp                 =  /usr/bin/cpp
> include             =
> integrator          = steep
> nsteps              = 50000
> emtol               = 0.01
> nstcgsteep          = 1000    ;step for cg correction ,the larger the more accurate
> nstxout             =
> nstvout             =
> nstlog              = 100
> nstenergy           = 10
> nstxtcout           = 100
> nstlist             = 10
> ns_type             = grid
> rcoulomb            = 1.4
> coulombtype         = pme
> fourierspacing        = 0.12
> pme_order        = 4
> rvdw                = 1.4
> rlist               = 1.4
> DispCorr        = enerpres
> constraints         = none        ; none,hbonds,all-bonds,h-angles,all-angles
> cutoff-scheme   =Verlet  ; GPU running
> constraint_algorithm  = Lincs
>
>
>
>
>
> but it stopped after 15 steps.....
>
>
>
>
>
>
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e-02
>     Number of steps    =        50000
>
> Energy minimization has stopped, but the forces havenot converged to the
> requested precision Fmax < 0.01 (whichmay not be possible for your system).
> It stoppedbecause the algorithm tried to make a new step whose sizewas too
> small, or there was no change in the energy sincelast step. Either way, we
> regard the minimization asconverged to within the available machine
> precision,given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, butthis is often not
> needed for preparing to run moleculardynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.1#
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 0.01.
> Potential Energy  =  3.4943549e+18
> Maximum force     =            inf on atom 23533
> Norm of force     =            inf
>
> NOTE: 22 % of the run time was spent in domain decomposition,
>        6 % of the run time was spent in pair search,
>        you might want to increase nstlist (this has no effect on accuracy)
>
>
> gcq#154: "Rub It Right Accross Your Eyes" (F. Zappa)
>
>

Your system has severe atomic overlap.  You have infinite force on atom 23533.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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