[gmx-users] Steepest Descents converged to machine precision
Mark.Abraham at anu.edu.au
Mon Apr 27 10:29:59 CEST 2009
nitu sharma wrote:
> Dear Mark
> I explain you what I want to ask . I give you a detail of my processing -
> * step for packing lipid around protein-
> 1. concatanation of protein and lipid bilayer in proper orientation- I did.
> 2.Inflate the bilayer by using inflategro script with scaling factor 4
> and cutoff 14- I did .
> there is 8 lipid removed in this process and a/c to that I have
> update my topology file .
> 3. Energy minimisation by applying strong position restrain on protein
> the force constant=100000
> problem occur here is-
> Step= 344, Dmax= 1.8e-05 nm, Epot= 4.29315e+06 Fmax= 1.02525e+05,
> atom= 4615
> Step= 349, Dmax= 1.4e-06 nm, Epot= 4.29315e+06 Fmax= 9.86524e+04,
> atom= 4615
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> Double precision normally gives you higher accuracy.
> writing lowest energy coordinates.
> Steepest Descents converged to machine precision in 350 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = 4.2931510e+06
> Maximum force = 1.0252509e+05 on atom 4615
> Norm of force = 1.3668822e+03
These are so large or positive that your starting structure is grossly
broken. You need to find out why. Look at the structures at each point
of your procedure.
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