On Fri, 2015-03-13 at 13:54 -0400, Jonathan Gough wrote:
> Attached is the .diff file.
Oh. I take that back. These diffs look like round-off issues with the
CHARMM charges (the multiplication factor CHARMM uses is slightly
different than the one that Amber uses).
These diffs look fine to me. Admittedly, ParmEd uses a method to
convert the Amber scaling to CHARMM scaling that can lose precision, but
the diffs you're seeing will have no measurable effect on simulation.
All the best,
Jason
>
> On Fri, Mar 13, 2015 at 1:52 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I am getting 26 errors when I compile AmberTool14:
> >
> >
> > possible FAILURE: check prmtop.new_type.dif
> > possible FAILURE: check prmtop.NBFIX.dif
> > possible FAILURE: check prmtop.new_chg.dif
> > possible FAILURE: check final.prmtop.dif
> > possible FAILURE: check md3_cpout.pH_4.50.dif
> > possible FAILURE: check pH_2.00.calcpka.dif
> > possible FAILURE: check pH_2.50.calcpka.dif
> > possible FAILURE: check pH_3.00.calcpka.dif
> > possible FAILURE: check pH_3.50.calcpka.dif
> > possible FAILURE: check pH_4.00.calcpka.dif
> > possible FAILURE: check pH_4.50.calcpka.dif
> > possible FAILURE: check pH_6.00.calcpka.dif
> > possible FAILURE: check pH_7.50.calcpka.dif
> > possible FAILURE: check pH_2.00.calcpka.dif
> > possible FAILURE: check running_avgs.dat.dif
> > possible FAILURE: check running_avg.dat.dif
> > possible FAILURE: check running_pKa.dat.dif
> > possible FAILURE: check chunk.dat.dif
> > possible FAILURE: check chunk_deprot.dat.dif
> > possible FAILURE: check chunk_pka.dat.dif
> > possible FAILURE: check cumulative.dat.dif
> > possible FAILURE: check cumulative_deprot.dat.dif
> > possible FAILURE: check cumulative_pka.dat.dif
> > possible FAILURE: check pop.dat.dif
> > possible FAILURE: check conditional.dat.dif
> > possible FAILURE: check conditional_chunks.dat.dif
> >
> >
> > The errors in the .diff file aren't "that big" (I could be wrong) but
> > unfortunate we are seeing some major differences in the calculations we are
> > doing.
> >
> > I didn't write the code that does the calculations, but I am 99.9% sure
> > that it is the errors in...
> >
> > possible FAILURE: check prmtop.new_type.dif
> > possible FAILURE: check prmtop.NBFIX.dif
> > possible FAILURE: check prmtop.new_chg.dif
> > possible FAILURE: check final.prmtop.dif
> >
> > that are causing the problems. essentially we are doing a short simulation
> > on a single frame with and without a single water and comparing the
> > difference in energy.
> >
> > we have 2 machines that are essentially identical. one compiles both Amber
> > and AT perfectly and the other does not... I check the gfortran versions
> > and the g++ versions and they are the same.. not sure what else I should
> > check.
> >
> > Both versions have the latest updates for Amber and AmberTools:
> >
> > AmberTools version 14.26
> > Amber version 14.10
> >
> > If you need more info, please ask. Thanks.
> > Jonathan
> >
> >
> >
> >
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 13 2015 - 12:30:04 PDT
