[gmx-users] RPM and double precision

Casey,Richard Richard.Casey at ColoState.EDU
Tue Feb 3 20:47:36 CET 2009


I'm not sure if we really need double precision.  Frankly, I would rather not fool with it.  However, when we run 

pdb2gmx -f compound4.pdb -p compound4.top -o compound4_a.pdb
grompp -f compound4.mdp -c compound4_a.pdb -p compound4.top -o compound4.tpr -zero
mdrun -v -s compound4.tpr -o compound4_traj.trr -c compound4_minimized.pdb -e compound4_ener.edr -g compound4_minimized.log

it returns after 6810 time steps:

"Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
Double precision normally gives you higher accuracy."

We've tried other step sizes, etc. with no luck.  The initial compound structure is very close geometrically to the energy minimized structure so it seems like it should converge to the optimized structure.


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