[gmx-users] energy minimization output

[Erik Marklund]

26 sep 2012 kl. 08.16 skrev Shima Arasteh:

> Dear all,
> 
> My system contains lipids, protein and water.
> I want to energy minimize it, so ran grompp:
> 
> 
> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
> 
> and then:
> # mdrun -v -deffnm em
> 
> 
> The output is:
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =        50000
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf, atom= 518
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> 
> 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.
> 
> Back Off! I just backed up em.gro to ./#em.gro.3#
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  2.3000388e+17
> Maximum force     =            inf on atom 518
> Norm of force     =            inf
> 
> 
> Why the maximum force and norm of it is not written? I repeated it for a few times, but no difference.
> 
> 

It's written. Unfortunately it's infinite.

> 
> Thanks for your suggestions in advance.
> Sincerely,
> Shima 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html