[gmx-users] Increasing machine precision

[Erik Marklund]

> Hello,
>
> Is there a way to continue minimizing after reaching machine 
> precision? Emtol and the number of iterations are sufficient to continue.
> I am assuming that reaching machine precision means that the gradient 
> of change from one iteration to another has become so small that 
> further minimization will not improve the structure. Is this correct? 
> If so is it possible to change the cut-off point for this gradient?
>
> Thank you in advance, have a nice day,
> Abdullah
The machine precision is the limit where the computer can't add a small 
number (e.g. the gradient) to a larger number (e.g. the coordinates). 
You could try using double precision, where your computer uses twice the 
number of bits to store the floating point numbers. I wouldn't bother 
doing that though, because the energy minimization is normally just used 
to releave structural strain from your system so that your md simulation 
won't crash due to enormous forces.

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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