Thanks guys.
Both Tom's and Mark's suggestions will fix the problem. The reason it did not
work before now in my case, was that the molecules were almost overlying
(almost same coordinates in structure file), thus the inf values I got.
I created some distance between them along one axis and was able to move on
with EM and simulation.
Rgds
John
> From: [EMAIL PROTECTED]> Subject: Re: [gmx-users] Step size too small> Date:
> Mon, 20 Aug 2007 10:07:09 +0200> To: gmx-users@gromacs.org> > > 17 aug 2007
> kl. 21.46 skrev TJ Piggot:> > > Hi,> >> > 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?> >
> /Erik> > > Hope this helps> >> > Tom> >> > --On 17 August 2007 19:02 +0200
> Per Larsson <[EMAIL PROTECTED]> > > 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>
> >>> >>> >> __________________________________________________> >> See what
> you’re getting into?before you go there See it!> >>
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> http://www.gromacs.org/mailing_lists/users.php> >>> >>> >> >> >> >
> ----------------------> > TJ Piggot> > [EMAIL PROTECTED]> > University of
> Bristol, UK.> >> > _______________________________________________> >
> gmx-users mailing list gmx-users@gromacs.org> >
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> _______________________________________________> Erik Marklund, PhD student>
> Laboratory of Molecular Biophysics,> Dept. of Cell and Molecular Biology,
> Uppsala University.> Husargatan 3, Box 596, 75124 Uppsala, Sweden> phone: +46
> 18 471 4537 fax: +46 18 511 755> [EMAIL PROTECTED]
> http://xray.bmc.uu.se/molbiophys> > >
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