Dear Ran,
I'm still unsure of why I sometimes can get double-precision output
and sometimes not. I can't find what I'm doing differently in each
case, however I now know what to look for in order to be sure that I'm
getting what I need. Obviously, the need for double-precision stems
only from the need to minimize the structure well before calculating
the Hessian. When I get a maximal force of more than 1E-6 I will get
some negative eigenvalues (which the program sets as zero) and some
other eigenvalues which are nearly zero. In all, there are six such
eigenmodes which I disregard as rigid-body degrees of freedom (3
translational and 3 rotational). The next modes have larger positive
eigenvalues.
As for the fix in eigio.c: I made lines 110-112 into COMMENTS (they
were not comments in the original file in the source). I recompiled
the entire program (didn't know at the time that I can "make" only one
function). Now the g_anaeig_d works fine (as best as I can tell).
Thank you so much for all of your help!
Inon.
Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
Inon Sharony wrote:
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).
What did you have in the input?
In any case if you get 6 zero frequencies and the rest are positive
you're probably fine.
I also wouldn't mind a clearer explanation of how you fixed
bugzilla
168 (see my request at
http://www.gromacs.org/pipermail/gmx-users/2008-August/035543.html).
Which lines did you add, and which did you change to comments in
eigio.c ?
The message from Tsjerk seems pretty clear. You can uncomment lines
110,
111 and 112 in eigio.c and recompile g_anaeig:
make g_anaeig
If everything went fine, you'll get a new executable for g_anaeig,
which
you can then copy to where you had the original version.
Ran.
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