[gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

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" <r.friedman at bioc.uzh.ch>:

> 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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Inon   Sharony
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