[gmx-users] Energy minimizations with gmx3.2

[Marc Vogt]

Thanks David,

I was actually doing steepest decents followed by conjugate gradient before.
Looks like the l-bfgs minimizer works really well.  Couldn't find
a literature reference in the 3.2 manual.  Is it there and I missed it?

thanks,


Marc

> 
> On Mon, 2004-05-17 at 17:10, Marc Vogt wrote:
> > Thanks Erik
> > 
> > The minimization under GROMACS 3.2.1 using l-bfgs converges whether or not 
> > I use switch interactions.  Any comments on that?
> 
> your tolerance is still 1000. You can lower it to 1 with this minimizer.
> 
> > 
> > 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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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone:  +46 18 471 4205  fax: +46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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