[gmx-users] More EM Questions.

[Christoph Freudenberger]

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
[snip]
> 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?

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