[gmx-users] Step size too small
erikm at xray.bmc.uu.se
Mon Aug 20 10:07:09 CEST 2007
17 aug 2007 kl. 21.46 skrev TJ Piggot:
> 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.
Yes. Just removing bonds in the top-file is not a good solution.
Breaking bonds changes the electronic structure of the molecule,
which in turn is represented by different atom types, so you would
need to change them as well, depending on the force field. Have you
tried the -nomerge option for pdb2gmx?
> Hope this helps
> --On 17 August 2007 19:02 +0200 Per Larsson <per.larsson at sbc.su.se>
>> Check out
>> 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
>> 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.
>> See what you’re getting into?before you go there See it!
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> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> gmx-users mailing list gmx-users at gromacs.org
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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