Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp:
# grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added "constraints=none" to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Thanks in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
