[gmx-users] single-precision *.tpr data after a double-precision run

Inon Sharony InonShar at post.TAU.ac.IL
Thu Aug 7 15:50:14 CEST 2008

I checked the *.trr, it does in fact show the coordinates in  
double-precision (as opposed to the output *.tpr file). I don't know  
why this is, but as long as I get a decent enough max. fore (i.e.  
~1E-05) I'll just leave it at that. I didn't see anything relevant in  
the *.edr file, so I'll just include the *.trr every time I run NMA.  
The em step is not specified in the nm.mdp file, so I guess I could  
add it (and specify 1E-05) and I hope that will help.

Thanks again.


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

> Inon Sharony wrote:
>> so it's an improvement of more than 6 orders of magnitude! Could
it be
>> that the *.trr file have the coordinates in double-precision?
> Right.
>> Not to be petty, but still, I had a max. force of
>> using the minimization procedure, and the Hessian calculation only
>> 4.32762e-04. That's still an order of magnitude that does not
>> from the energy minimization step to the Hessian calculation step.
> Sounds strange. You can try to save the forces in the trr and see
if it
> gets more accurate. Also, do you use the same emstep as in the em
> I guess this determines the displacement in NMA as well.
> Ran.
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Inon   Sharony
ינון     שרוני
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