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

[Inon Sharony]

Quoting "Ran Friedman" <r.friedman at bioc.uzh.ch>:

> Inon Sharony wrote:
>> 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.
> If the info in the .gro file is in single precision, the values in
the
> .tpr will be with 3 significant digits and then zeros. Sorry if I
wasn't
> clear about this.

How do I get a *.gro file in double-precision, then? The  
configurations given by the PRODRG server are in 0.000 format, and  
still I've at least once managed to get double-precision calculations  
out of them (right now I'm working on a file for a Pentane molecule,  
originally downloaded from PRODRG, but everything's in  
double-precision). I have to be doing something wrong, if I get  
single-precision some of the time and double-precision other times...


>> 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).
> Oops. I had the lines already commented, probably because I
corrected
> this on my machine some months ago.
> Ran.
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Inon   Sharony
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