[gmx-users] Re: Minimization not converging
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 12 16:07:25 CET 2009
Jack Shultz wrote:
> I should have included some output
> Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439
> Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> writing lowest energy coordinates.
> Steepest Descents converged to machine precision in 34 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -1.4354568e+06
> Maximum force = 6.9535597e+10 on atom 25439
> Norm of force = 4.5592896e+08
> More details here.
From your pdb2gmx output, it looks like you have some lousy starting geometry
in whatever structure you're processing:
Try to run EM on that structure before solvating (i.e., in vacuo) , because you
probably have lots of steric clashes with the solvent arising because of
improper protein geometry.
> On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz
> <jshultz at hydrogenathome.org> wrote:
>> I think that my minimization are not running long enough. I've been
>> following the parameters in tutorials but it seems like they all die
>> at 34 steps
>> I've been using these tutorials
>> Its been the same case for me regardless to whether I use Windows or
>> Linux platforms. Are there settings I can use to make the simulation
>> minimize longer or is this case where I need to have double precision
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users