[gmx-users] EM comparison

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 26 01:01:30 CEST 2006

Kushal Seth wrote:
> Hi all !
> I was doing EM for a bilayer. While using the mdp file containing only
> the energy minimization terms my energy is minimized  but i get the
> following  :
> Converged to machine precision,
> but not to the requested precision Fmax < 100
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> writing lowest energy coordinates.
> Steepest Descents converged to machine precision in 111 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -5.2422903e+05
> Maximum force     =  3.8640459e+03 on atom 18141
> Norm of force     =  7.6843672e+04
> What are the implicationsof Fmax > 100 in my case.

You've selected a criterion for terminating the EM that wasn't able to 
be satisfied on the current system because the energy converged to 
machine precision before the forces got small enough. This is not a big 
deal so long as those forces aren't huge - sorry I can't define huge. 
Have a look at your system to see that it still looks physical and try 
some alternate minimization algorithms.

> Also if i modify
> the mdp file and increase the terms to contains the temp and pressure
> coupling terms my energy comes out to be the same but at the same time
> my Fmax also converges to < 100. WHY SO?

Evidently, these terms are having no effect. Since none of your atoms 
have velocities in an energy minimization, how would you like to define 
temperature and pressure so that they can be coupled? :-) Please read 
the introductory pages in the gromacs manual until you understand the 
difference between EM and MD.


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