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.
Mark
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