[gmx-users] equilibration

Anton Feenstra feenstra at chem.vu.nl
Tue Aug 12 09:01:02 CEST 2003

Arvid Soederhaell wrote:
> Hi all
> I am trying to equilibrate a membrane-peptide-water-ion system but it
> doesn't work. Gromacs is quite new to me so the questions might be stupid.
> The system should already be quite well equilibrated since it comes from
> dynamics run using amber. The only thing that is done is making a new
> periodic box and adding hydrogens. 
> I have tested to do a steepest descen minimization and the error message
> in the .log file is:  
> --------------------------------------------------------------------
> Stepsize too small (6.10352e-07 nm)Converged to machine precision, 
> but not to the requested precision (1) 

When the energy doesn't go down in an EM step, Gromacs decreases the step
size (i.e. the amount by which the atoms are moved along the energy gradient).
At some point, you drop below the arithmetic precision of the calculation,
i.e. the stepsize is so small that the coordinates do not change at all any
more. This is detected and the EM stops. This means that, although forces
are still high (higher than you set as convergence criterium), energy won't
go down. You're in a local minimum.

> You might need to increase your constraint accuracy, or turn off
> constraints alltogether (set constraints = none in mdp file) 
> Steepest Descents did not converge in 15 steps
>   Potential Energy = nan Maximum force:  1.45952e+10

There is something defenitly not right with your coordinates, to
produce 'nan' energy, and a maximum force of 1e10! (For comparison,
I can generally minimize to maximum forces around 1e3.)

What do you mean by only 'making a new periodic box'? Did you re-solvate
your protein/bilayer? Did you 'trim' your system (i.e. removed a slice at
the edges) to get a smaller bilayer sheet and/or water box? Did you maybe
only edit the box size, without touching the atoms or coordinates?


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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