[gmx-users] Increasing machine precision

Erik Marklund erikm at xray.bmc.uu.se
Tue Feb 8 11:00:09 CET 2011

> 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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