[gmx-users] Normal Mode Analysis in Double-Precision
InonShar at post.TAU.ac.IL
Mon Aug 4 11:12:20 CEST 2008
This is exactly the point - I get only three significant digits.
Although I performed the entire procedure in double-precision. The
convergence to 5E-4 DID occur in single-precision, I just thought it
wasn't good enough (the program recommends 1E-5 and when
double-precision works for me I got 1E-6 with the files you sent me).
I also wouldn't mind a clearer explanation of how you fixed bugzilla
168 (see my request at
Which lines did you add, and which did you change to comments in
Thanks, and have a great week.
Quoting "Ran Friedman" <r.friedman at bioc.uzh.ch>:
> Hi Inon,
> Check the files after EM. How many significant digits do you have?
> guess you wouldn't get a convergence to 5E-4 with single precision.
> my experience it may be worth to run several cycles of EM, say CG
> then L-BFGS to get better convergence.
> Inon Sharony wrote:
>> I now performed:
>> make distclean
>> ./configure --disable-float
>> make install
>> make links
>> All executed without problems. Now I no longer have segmentation
>> faults (thanks David!), however the energy minimization still does
>> achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04 for
>> pentane). When I looked in the *.tpr file I saw that the
>> are still given to three significant figures, meaning that the
>> two decimal places (fourth and fifth to the right of the decimal
>> point) are always zero. I understood from Ran that this means the
>> is still in single-precision. How could this be?
>> Can anyone please help me get proper, double-precision from my
>> Thanks, and have a glorious week.
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