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
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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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
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