Casey,Richard wrote:
Berk,
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."
You may find the following useful:
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision
Fmax < 1 is a fairly stringent minimization condition (depending on what the
system is); that may be the reason you're seeing this message.
-Justin
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.
--------------------------------------------
Richard
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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