[gmx-users] More EM Questions.

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Tue Jul 15 09:36:01 CEST 2003

Joel DeWitt wrote:
> gmx-users:
> When I run EM on my DPPC monolayer (just 30 lipids), I get peculiar 
> standard output:
> Steepest Descents:
>   Tolerance         =  1.50000e+02
>   Number of steps   =         1000
> Step=    0, Dmax= 1.0e-01 nm, Epot= -2.81451e+03 Fmax= 6.07879e+02, atom= 1158
> Step=    7, Dmax= 1.6e-03 nm, Epot= -2.82194e+03 Fmax= 1.15606e+03, atom= 1484
> Step=    8, Dmax= 1.9e-03 nm, Epot= -2.86810e+03 Fmax= 1.09084e+03, atom= 1484
> I've written EM algorithms from scratch before and GROMACS obviously is 
> not being thorough in its energy minimization.  Sure, the potential 
> energy is being reduced overall, but it doesn't seem like EM is 
> examining the system as a whole; just a handful of atoms.

I always understood the em output to refer to the atom that is affected by Fmax and
not that this was the only atom to be changed.
Is this correct?

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

More information about the gromacs.org_gmx-users mailing list