[gmx-users] Step size too small

TJ Piggot t.piggot at bristol.ac.uk
Fri Aug 17 21:46:58 CEST 2007


I do not think that what Per suggests is the problem, if you look at the 
potential energy after the minimisation this value is huge (and the other 
two values are inf!). The problem is most likely with your topology. As you 
say the two molecules have been successfully minimised on their own so I 
would suggest that your problem is with either how you edit the .top file 
or the distance restraint between the molecules. For my protein that has 
more than one identical chains pdb2gmx does not recognise them as one if 
you provide different chain identifiers in the pdb file, so doing this 
should hopefully stop you having to edit the .top file.

Hope this helps


--On 17 August 2007 19:02 +0200 Per Larsson <per.larsson at sbc.su.se> wrote:

> Hello!
> Check out
> http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan
> ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_
> precision
> Cheers
> /Per
> 17 aug 2007 kl. 18.28 skrev Sheyore Omovie:
>  Dear gmx-users,
>  I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited
> the .top file to remove the bonds created between the two molecules, I
> also added a distance restraint btw the molecules. (The 2 structures have
> been separately minimized). However, I get the ff message for EM run:
> 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.
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  1.0246325e+20
> Maximum force     =            inf on atom 1
> Norm of force     =            inf I would appreciate any advice on how
> to fix this.
>  Rgds
>  John
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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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