[gmx-users] Energy minimizations with gmx3.2

[David van der Spoel]

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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> 
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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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