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." 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
