Problem partly addressed. If I run normal modes in -nt 1, then I get the same force as after the minimization.
I'll file a redmine. On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts <mrshi...@gmail.com> wrote: > To follow up -- if I try to minimize again using -t, I get the same > low forces as in the minimization in the previous step. So it appears > to be something with what do_nm is doing, not with errors in the > output structure. > > On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts <mrshi...@gmail.com> wrote: >> When I minimize a structure, I can get down to the force max being <0.01 >> >> Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps >> Potential Energy = -5.12340607768673e+03 >> Maximum force = 6.68907856457542e-03 on atom 3029 >> Norm of force = 2.19978176343026e-03 >> >> kJ/nm. However, when I try to perform a normal mode analysis, it >> complains that the maximum energy is >30 kJ/mn. >> >> >> Non-cutoff electrostatics used, forcing full Hessian format. >> Allocating Hessian memory... >> >> Maximum force: 3.91984e+01 >> Maximum force probably not small enough to ensure that you are in an >> energy well. Be aware that negative eigenvalues may occur when the >> resulting matrix is diagonalized. >> >> I've restarted from the binary .trr output (-t option) , and I'm using >> double precision. Any suggestions as to why the force max is not the >> asme on restarting? Only difference is going from l-bfgs to nm. >> >> I've seen some older comments on this, but no resolution and nothing recent. -- 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
