[gmx-developers] double precision minimization accuracy limits.

Chris Neale chris.neale at utoronto.ca
Tue Jan 22 22:32:55 CET 2008

David.Osguthorpe at UCHSC.edu wrote:
> Hi,
> Im attempting to minimize a protein-solvent system (>10,000 waters) 
> using the double precision program
> to minimize structures dumped from a single precision dynamics run.
> Ive switched off all constraints, including switching to flexible SPC 
> waters, added switching functions to the
> LJ and coulombic potentials to make a smooth cutoff.
> However, all minimizations (conjugate gradients, l-bfgs)  all seem 
> termate to terminate at what I consider
> to be large derivatives for a double precision program.
Unless I'm missing something, this is a users-list question. Energy 
minimization is going to get stuck in a local minimum. The acid-test of 
a minimization is if the resulting structure can be used to start an MD 
> e.g.
> Polak-Ribiere Conjugate Gradients converged to machine precision in 
> 123 steps,
> but did not reach the requested Fmax < 0.01.
> Potential Energy  = -1.64197713818716e+06
> Maximum force     =  2.32094495259875e+02 on atom 31761
> Norm of force     =  6.19775726238427e+00
> Low-Memory BFGS Minimizer did not converge to Fmax < 0.01 in 1501 steps.
> Potential Energy  = -1.65198292382305e+06
> Maximum force     =  2.70928575898524e+02 on atom 25485
> Norm of force     =  6.58974288803592e+00
> Is there some step size variable I should be making smaller to allow 
> the minimizers to make even smaller
> changes to the coordinates (Im assuming from the message its at 10-12 
> changes or less).
> Am I expecting too much of the potentials, forces etc. to deliver 
> lower forces?
> In particular Id like to have the Maximum force under 10
> By the way I made some modifications to the tpbconv program to allow 
> me to pass full double precision coordinates
> to the program as otherwise writing out to a .gro file jumps the max 
> force and norm significantly and I dont
> see a way to continue from steepest descent with conjugate gradients 
> or l-bfgs without performing a new mdrun run.
> - and lbfgs seemed to take forever to work on its own and get nowhere 
> - cg was way below it in force/energy after
> far fewer iterations.
I don't see why you couldn't grompp your next energy minimization using 
-t .trr -e .edr but again, that should not be necessary.

> Thanks
> David
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