26 sep 2012 kl. 08.16 skrev Shima Arasteh: > 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 > > > Why the maximum force and norm of it is not written? I repeated it for a few > times, but no difference. > >
It's written. Unfortunately it's infinite. > > Thanks for your suggestions 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
