[gmx-users] Energy minimizations with gmx3.2

[Marc Vogt]

Thanks Erik

The minimization under GROMACS 3.2.1 using l-bfgs converges whether or not 
I use switch interactions.  Any comments on that?

Without Shift:
---------------------
Step 16, Epot=-1.610425e+05, Fnorm=1.018e+02, Fmax=9.072e+02 (atom 5925)

writing lowest energy coordinates.

Back Off! I just backed up crabpsm.gro to ./#crabpsm.gro.5#

Low-Memory BFGS Minimizer converged to Fmax < 1000 in 16 steps
Potential Energy  = -1.6104255e+05
Maximum force     =  9.0724634e+02 on atom 5925
Norm of force     =  1.0181800e+02

With Shift:
---------------------
Step 106, Epot=-2.055670e+05, Fnorm=2.954e+01, Fmax=6.882e+02 (atom 1185)

writing lowest energy coordinates.

Back Off! I just backed up crabpsm.gro to ./#crabpsm.gro.6#

Low-Memory BFGS Minimizer converged to Fmax < 1000 in 106 steps
Potential Energy  = -2.0556705e+05
Maximum force     =  6.8819617e+02 on atom 1185
Norm of force     =  2.9543177e+01

gcq#60: "I Could Take You Home and Abuse You" (Magnapop)
(Nice to see the hometown band represented!)



The system is approximately 12,000 atoms.  What would you reccommend?
l-bfgs also converges to Fmax < 100 for me without problems.


thanks,
Marc



> 
> HI Marc,
> 
> If you haven't already, you might want to try "l-bfgs" as a minimizer, 
> in combination with switch or shift interactions. (The reason for this 
> is that bfgs builds an iterative approximation to the inverse hessian, 
> and if you use cutoffs it changes between steps).
> 
> Still, 1000 kJ/mol sounds a bit high. How big is the system?
> 
> Cheers,
> 
> Erik
> 
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