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

Inon Sharony InonShar at post.TAU.ac.IL
Thu Jul 31 16:04:15 CEST 2008

Hi Ran.
I looked up your suggestions, and got the following:

0. The parameters in the *.tpr file appear in " 0.00000000e+00 "  
format. How can I tell if this is a float or double? Also, I could not  
see if the position coordinates of the molecule appear in the *.tpr  
file (and if so, if they are in double-precision). Where do the  
coordinates appear? (in the *.gro file only?)

1. I do not get any step*.pdb files after the mdrun. In fact, I skip  
the *.pdb file altogether (using PRODRG). Could this be a problem?

2. The simulation is done in vacuo.

3. I examined the input *.gro file (as well as the single-precision  
mdruns) using ngmx, and it looks great for those runs that work (i.e.,  
single precision).

I will now try repeating the whole minimization-NormalMode process for  
a simple diatomic, to see if I have any problems. Could you send a  
working set of files for me to compare with? Assuming you've run  
Normal Mode analyses in the past...

Thanks very much again,


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

> Inon Sharony wrote:
>>  Hi Ran, thanks for the reply
>> I ran "make tests" after compiling with double precision, and it
>> out fine.
>> Could it be that this, second, compilation might have caused some
>> problems -- I had GROMACS compiled in single-precision, and it
>> fine -- could compiling in double-precision after the initial
>> single-precision overrun some files? I'm not sure anymore...
>> Also, the grompp in double-precision works fine (no warnings,
>> but I get the segfault from mdrun (also in double-precision).
>> Sometimes this happens in the first minimization step, and
>> in the second. I was told that this might hint that the input
>> (e.g. the *.gro file) were input in single- and not
>> However, since the files have coordinates written in nanometers to
>> four significant digits, I can't see how the input numbers could
be in
>> single or double precision. It was suggested that I insert a
"print to
>> screen" line in the source code immediately after the *.gro file
>> read, to see if the printed data is in single-precision or
>> double-precision format. What do you think?
> The tpr should contain the data in double precision. You can check
> with gmxdump.
> Other things that you may want to consider:
> 1. Do you get step*.pdb files after running mdrun? This may point
out to
> something wrong in the input.
> 2. Are you using a solvated system? Normally NMA is done in vacuo,
> with some scaling of the dielectric.
> 3. Did you examine the system that you use in the input? Does it
> sense to you?
> Ran.
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Inon   Sharony
ינון     שרוני
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